From 9cc618090cc153bbb443dfe0ba6e7d4ea2f3ae99 Mon Sep 17 00:00:00 2001 From: Jennifer Chang Date: Thu, 27 Feb 2025 18:09:45 -0800 Subject: [PATCH 1/7] Add Mopeia virus as an outgroup Mopeia virus is another Old World arenavirus. Picked Mopeia after glancing through paper https://pmc.ncbi.nlm.nih.gov/articles/PMC112216/ Picked the RefSeq entries for Mopeia from NCBI Virus https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?SeqType_s=Nucleotide&VirusLineage_ss=Mammarenavirus%20mopeiaense,%20taxid:3052320&SourceDB_s=RefSeq --- phylogenetic/defaults/gpc/outgroup.fasta | 2 ++ phylogenetic/defaults/l/outgroup.fasta | 2 ++ phylogenetic/defaults/s/outgroup.fasta | 2 ++ 3 files changed, 6 insertions(+) create mode 100644 phylogenetic/defaults/gpc/outgroup.fasta create mode 100644 phylogenetic/defaults/l/outgroup.fasta create mode 100644 phylogenetic/defaults/s/outgroup.fasta diff --git a/phylogenetic/defaults/gpc/outgroup.fasta b/phylogenetic/defaults/gpc/outgroup.fasta new file mode 100644 index 0000000..c3d0100 --- /dev/null +++ b/phylogenetic/defaults/gpc/outgroup.fasta @@ -0,0 +1,2 @@ +>NC_006575 +atggggcagatagtcaccttctttcaagaggtgccacacatccttgaagaagtgatgaacattgtgctgatgaccctctcaatcttggccatcctaaagggcatctacaatgtgatgacctgtggaatcatcggtttgataacatttttgttcttgtgtgggagatcatgctcaagcatctataaggacaactatgagttcttctctttcgacctcgacatgtcttcactgaatgcaacgatgcctctctcctgctcaaagaacaactcccatcactacatccaagttgggaatgagacaggcctagagctgacattgacaaacactagcataattgatcataagttttgcaacctgtctgatgctcacaggaggaatctttatgacaaagcacttatgtcaatcttgacaacattccacctaagcattccagattttaaccaacatgaggcaatgtcatgtgattttaacggagggaagatctcagttcaatacaacctgtcccactcaaattatgtggatgccggcaaccactgtggcactattgcaaatggcattatggatgtttttagaagaatgtattggagcacctccctttcggttgcctctgacataagtgggactcaatgcatacagaccgattataagtatttgattattcagaacacatcatgggaggatcattgcatgttctcaagaccctcacccatgggatttttaagccttctgtcacagagaaccaggaatttctacatctcaagaagacttttgggtctttttacatggactttgagtgactcggaagggaacgacatgccaggtggttactgtctcacaaggtctatgctaatagggcttgatctgaaatgctttgggaacactgccattgcgaagtgtaatcaggcacatgatgaagaattctgtgacatgctccgcctttttgattttaataaacaagcaattagcaaactgaggtctgaagttcagcagagcataaatttgataaataaagctgtcaacgccctcatcaatgatcaactggtcatgaggaaccatttgagagatctaatgggtattccttattgcaactactctaagttttggtacttgaatgatactaggacagggagaacatccctcccaaagtgttggcttgtgaccaatgggtcatacctaaatgaaacccagttctcaacagaaattgagcaagaagccaataacatgttcactgacatgttgaggaaggagtatgagaaaaggcagagcacaacacctctggggttagtagatctttttgttttctccactagcttttatttgatctccgtgttcctccacctaatcaaaattccaacacatagacacataaaaggcaagccttgcccgaaaccacacagactcaatcacatggcaatctgttcctgtggcttctataagcaaccaggtctccccacacaatggaaaaggtga diff --git a/phylogenetic/defaults/l/outgroup.fasta b/phylogenetic/defaults/l/outgroup.fasta new file mode 100644 index 0000000..4f385cd --- /dev/null +++ b/phylogenetic/defaults/l/outgroup.fasta @@ -0,0 +1,2 @@ +>NC_006574 +atggggaaaacgcagtccaagggacagcccagcacaaatctcctcaaggagacagaaccaaggcatccagtaataccagatgccaggggaactggccctgaattctgcaagagctgctggttcgaaaggagggggttagtcaggtgcaacgatcactacctatgtttgaactgtcttacacttttacacacagtgtcagataggtgccccatctgcaaacacaaactacccttcagactagagctccagacccagccgacagcaccaccagaaatcccaccatcccaaaatcccccaccctacagcccctgaggcagaactccgccccgaagcccctcccaaacacccctcccctcccccccggggggaccccccgccggggctccccccggggggagatgcgcgagctgttctcggagcacctactcaatgtcgaggggaggccccacctcttcaaagaggggcctgcacagcctccctcttaatctaaacttcccctctgaagactggatcatcagtgaagcctgcgatctactgtagcagagactatagcctttaaaatctgcccagaagtcaattccggagaacactctagtaaggaagttttcgtagccttcaggcatgcatcgtcccacaacccctataatatcaagttgtagccagtgtagtccttggtccattctggatctcagcatcttgctcaaagatctctccaagatttcggaatgatcctccattagctcaccaataaaaacattaagatcctggtcatggatgttggggttgaagggcaggagtttcctggtcccttcaataaggtatcctgagtcaacaactaaggggatttcaacatgctcaggccctatatgcgtgaaatcatgttcctccaggtccaggatctcctcattcaataagacggacaagggtatcacatcaggaatgggggaactatccctcaagtagtcacaaatattttcagtggacagcaaccaaattgatgtggtttcccttttaaaccatgtagatgtctgtgcaactctccagcaatctttaattgcggatctttgaacactaccactgtaagttacatcaagggaatgaggcttgaataatccaccttccaacaccacccctttgaaaaggaggtggagactaaatttctctttcaatgattcaccctgacttctcacctgaaaatttactgtgacagaaatttgaacgctcccaacactgaggtcggcaaaagcttcaagcagctcacttaccgactcaaagacgtgctgctcggttaatcctgatgctatgagctgtcctaagtttagaattgctggtgcacattcaaagtccagccaagcataacctgagtaaagatcatgcctgtacatgggtctttcaacacccttataaataaccttttctataaaagaagaaaaggggccgaggttgtcaagcccttccgactcaggaattgaagatctatgtggaaaccaagtaaaagaacctaaagtcctgcttgttgcaacgaatggtctgatgaaggactcaaagtagatttgtctcaggaaattttgtaccacatcataagtggtcaccaccctttcatccgtgattgggagatgagacctctcatgtgctattgctaaatctgaagacagaaccacataatgctcttctctcttccacttgacaacatgagaaattaatgacattgcctcacaattcacatctagaaccacacaaagatcaagaaacttaatccttggtgtccacctcattttcgttgatgctaggtcactcatgaagggcaagaggtgtctctcaaatagagatgggtaaagtcttctgaatgagtgaataatatggttaaaccccaccttgtcttccaagagttttgtggtagtgggcttcattgggaaatagtcacatggcttgaagggaattgaggatgttttctccttcactttgggttcacccaacacccaggaacccagctcaagtgatgtagataaggctatgcagaagtaatcccaaaggacaggtctcaagaaacctaacgcttcctcagctgcctttgtgtgctccttacccaagatccaaagatcgacgcccttaactttcaagctggaaacagaatccaatgctgacagtcttgaaactaatgattttatataggcggtggacctatctgagaatcgaacacatttgctacctagtgtcttgcaaagacctatgaaacctgatgctatcccactctgaaaggcacttttgttgacggcttcacagagcaacttttgtgcccctcttgtgaaattagaggataacttgctttgcaatgttttcaccaaggtaggcagtttttcttccccgagttcaacagcacctgtgtaaatgaccttctgtctcatgaccatctttaaagggtgatgagttgtcaaattaagccaacacaccgataaatcctcttctgagagggtgtcatcaccaacaaggctggtaagtttcttgaaggaatctgcggggtctcctgacaagtagatggctgtgaattcttcatgaagctctcctaatttcagcttattaaaaactgtccttaggaccttcctaactttctgagtgctttctggtaggattgcctcaatgttcctcataatcctatagcccctattgccatcaacccaatctttaacatcagaatccaaaaacaacaagaaaggatcaatgggatattgtgcatatctaagtagattcagtgttctctcctgaatagcgttacatagtgtgacaggcacaccattggccactgactgatcaatgatagtgtcaatagtttcagctaattgatgtggctccttacacttaacgttgtggagggcggcagccacgaatttcgttaacaatggaacttcatcaccccagacataaaaccttgatttgaactcagcaacaaatgaaccaataacactctttggactgatgaatttattcaattgatcacttaggaaatagtgaaattctagaatggcttggaattcctcaggctcatttgagagtaaatctgaaagatccttgccaaatagtgatatttgatcatcactagaggtatatgaatcaacttcatcttcaaatagacacttaatgcaataatttatgaatctctcactcactagaccgtagaagtcagaagcattgtgcaagatcccttgccccatgtcaattattgagctgagatgtgatggtattctgttttgtttaaagtattcaaagaagaaagcttctgttgacgtttggtggagtgattttttcaaacctaacctagacttaagataagatctcatcattgcattcacaacattgaaaggtacctcaattaacttgtgaatgtgccacgacagcaaagtggacacgtaatccttactttttatgtcctctatatcatctcttgtctcccatcgcaaattttgaagaaacaccaggaaaagaaaaggggacatcataggcccccacttgctgtgatcgaggctataagagacctgacctagtgaaacattcaatttcatggctagaatggcattgtggaattccttttcattattaagacagctccctctatattgcttagttagtgcctcaaaataatcctcaattaggcgtgtgaacatttttgtcctcaggtcacctatataaagttccctgttccctccaacttgttctttgtaagataaggaaaacttgagccttccagtatcaggacccaaggatgtgtatgactgtggggattcttgactgtaaaaacataggttctttagaactgcagttgtacaatttgtcaatgacagtgctttacctaatgcctcagaattgctctctctttcactgatcctaacatcattcatcagcctttctctatcaatcttgaagtttaggcatttgtttttgtaatggctgtattttccagccaatttccctgcattcatctgaagaagtagtgacttgaagcactgaaaaaactgctggtcattgaatgttctggtggagacagcttgggtgatgcatgttattgggcaagagtccaaggaatccaaatagaaatactttgatcttaactccaaatccttaaaaaagcctttgcagatcatctcataagcatctccaggtagtagtgactcatcaaaatcttccaccatgtggtgtgctatctctgcctggatcagtctgtagtaaacacagcccacatcttcagtacctaaaaccttcctcaagtctgtcaaggacttctcctctgacccatttcccacagggaacttcctgtcatatctatacttctcaaggacgacatcaacagatttcttcacatcctctagacagtcaagtgcacaactatccaagaataactcatctaattcgtcaggagccccttgtgaattgggatttgaggaacctgacttcttccccacaacaaggtcactaatggccttttgcaccttataatcataatcctccttactcaagaggtatttagttttcctctggaatacctctgatagctggcaaacagaagcagccactagtttatcatgatcgtaataaagtatcctctctccgtcagtatacttattcacaaccacacttttgttgcttgcaaggtcaagagctgttgcacacccagcagtaactaatggatctttaaacccacttaggtcatctcctttcttgaaaagagagccattgttaaaagaagacgtcatcattgagaagaattttcttgacacaccaggaactttataagatattctgttgttactcatactggtttctttggataaaaatttgtttgctgattcaagcagcagcatcctttcatcttcatccccctcttcagatgggttgatgttaatactgtcaaactccaacttgggctccaaatacttctcaaagcacttaatctgatctgtcaacctatctggagtttccttagttataaaatgacacatgtatgataggtttaacacaaacttaaatctattagtcaacatagtgctcaccccttcacccaggatgatgttgagaatgctcctcaccacactatacaagaggtgctccggctctgttatgagatcctccctcaacttttccattaactgcttatggtggaagtctgaaacaaaggccattatgaagtatcgcagaccttgcaagaacttctgtgctcttttgctagggttcacaagtatgaggatcatggtgattttgagcaataattttaaagttttttgttgatctctgagttctatacattcagacaaccaactcatcatggtgttgatagtctcatagataacacagtgtgagaaaattgcaggaaaaaacctttttggatctgcatagaatgaacaaatctcccccttctcaggattgttaatggcataacattttgagcactctcctgttttctgataaattaagttgaaattcccgcttcccatgataaagctttgattaaaagcttccttacaacgtacacgtttgtaccttgcagcaccatactcattttgcctcactttggctactgatgatgtcttcattgaattcaccaatgccaaagagatgctagatagtcttctcaggtcttctatggaatcagcttccaactcaataagagggtaggggaattgattcccctcttctttctcatagctcattgttggctgaatccctcttttctccattaacataagcctctcgtaactgtcctcctccagtatatcttcctctttaacataatctctaaagcacaaactggcagaggataatgcctctttggcctttgtgaggagtttgtttatgatgtcaaagaatataagctcagatctctgacacagagttcctacacctcccttcttcttcattgcactcaccattctcctttcaatccactttttaaggtccttttgtgtttcttgtagtgacaccaatctgtcgttcacacttaagaatgaggagccaagccattctgatcctaacagctcgccgtgacatttaagatcctttaagtgggccaaaaggatgattgcgtcaaaagtcagcattagttttcttctggtgttcaataactttagtgattttattttattcaacagtgacttccatccaggcacagagctttggaagtgattctgcaagcagctgtctcgatcaactccctcttgcctataacggtcgtagtcaccatagagcgctgttaccataggcgaggattttacaaacctctcttttagaggatcaatctctgagggtgtgtccccctctctgtcaatataaaggttgttgaaatctctcaagagctgtcgcctatctgtcctgacaaattgtctttctatctcaccctctttaagcttattcctaaaagcatgaaattctgatacaatctcttttttcacatcaagaatggacattttgttattgatgcctctgtggcagagctccaacaccctctcataatgatcagatcgagaatctgtcaaaacattgaggctctcaatgcccgatgttctcactcctgcttttgttaaagattcacaaagccttgagtactcagattcttcaaacatttttgatgactgctgcgagaattcaagtaagctaaataggatatgcctaaacctctcattggcccattctggaaacaaatcagtgtagaaattggttctgccgtctatcaagggcaacagaatgatgtcaacagatgataagtcaggctttaaagactctagcttaatggtatcttctttatacttttgctcaaagtttattggtgaagtcctgacaaagcattccagtaatattaatgtgttcccactgaatttgaatccatctggcaccacaaatggtagaccagggcacagaacaccttgtctctgcagaaggatttcaacagaaaggtcttctgagttgtgctcacaaccattggctttgcaactgtctatctcaatacagagtgacaacaacttaaggccctcaattaatagcattctcggctctgtctgaactaggaaggctagcttctgttttgaaagcctctcatcctctaagaggtacctgctcacaagatctttgctctcggacagcaactcctccat diff --git a/phylogenetic/defaults/s/outgroup.fasta b/phylogenetic/defaults/s/outgroup.fasta new file mode 100644 index 0000000..5bd7f0d --- /dev/null +++ b/phylogenetic/defaults/s/outgroup.fasta @@ -0,0 +1,2 @@ +>NC_006575 +atggggcagatagtcaccttctttcaagaggtgccacacatccttgaagaagtgatgaacattgtgctgatgaccctctcaatcttggccatcctaaagggcatctacaatgtgatgacctgtggaatcatcggtttgataacatttttgttcttgtgtgggagatcatgctcaagcatctataaggacaactatgagttcttctctttcgacctcgacatgtcttcactgaatgcaacgatgcctctctcctgctcaaagaacaactcccatcactacatccaagttgggaatgagacaggcctagagctgacattgacaaacactagcataattgatcataagttttgcaacctgtctgatgctcacaggaggaatctttatgacaaagcacttatgtcaatcttgacaacattccacctaagcattccagattttaaccaacatgaggcaatgtcatgtgattttaacggagggaagatctcagttcaatacaacctgtcccactcaaattatgtggatgccggcaaccactgtggcactattgcaaatggcattatggatgtttttagaagaatgtattggagcacctccctttcggttgcctctgacataagtgggactcaatgcatacagaccgattataagtatttgattattcagaacacatcatgggaggatcattgcatgttctcaagaccctcacccatgggatttttaagccttctgtcacagagaaccaggaatttctacatctcaagaagacttttgggtctttttacatggactttgagtgactcggaagggaacgacatgccaggtggttactgtctcacaaggtctatgctaatagggcttgatctgaaatgctttgggaacactgccattgcgaagtgtaatcaggcacatgatgaagaattctgtgacatgctccgcctttttgattttaataaacaagcaattagcaaactgaggtctgaagttcagcagagcataaatttgataaataaagctgtcaacgccctcatcaatgatcaactggtcatgaggaaccatttgagagatctaatgggtattccttattgcaactactctaagttttggtacttgaatgatactaggacagggagaacatccctcccaaagtgttggcttgtgaccaatgggtcatacctaaatgaaacccagttctcaacagaaattgagcaagaagccaataacatgttcactgacatgttgaggaaggagtatgagaaaaggcagagcacaacacctctggggttagtagatctttttgttttctccactagcttttatttgatctccgtgttcctccacctaatcaaaattccaacacatagacacataaaaggcaagccttgcccgaaaccacacagactcaatcacatggcaatctgttcctgtggcttctataagcaaccaggtctccccacacaatggaaaaggtgaagaacaggggcacccccgagacccaccgccttcggcggtgggtctcgggggcctggagtgactgttccttgatggcctccacgacccaccgccagaggcggtgggtcgtggaggtgtcccttcttacaggacaactctgggaggacctgttctaaacaccaggtctctactcaagactggtctgggggttggaatttgtggactccctatgactgctgcttcaaacatgagacaatccagcaatgcacagtgtggtgtcacttcttctttgccacctctcttcttcttttgcgttacaatccccgtatgcattctacaaaggtgtttgtattcatcccagatcttatcctcaaattttcttgcatcgtctttctgcatggacacatcaatcagttttatgtccctcctgttctgggagtcaagaagctttctgatgtcatcagcaccttgacacgacaagaccatgttctttggcaggctctcaattacagcacttgtcaaccccggctgaactgagaataggtcttggatgtcaatgccatgagagtgtttggagtcttgtttgaattgtttaatgtctgttggttccctgtaaaaatgaatatactgaccattattaggttgatagatagctatctccacggggtcttcaggtctcccttctatgtcaatccatgtcttagcatttggatccaattgcaacatgctgtctttgagttccattgtctgagagtaggtcaaaccagcaggcatgccttgggcctgagcgagtctgttggagttacctttgtcaggctttgcattctgttgcacatcaccactcagatcaacagttgtgttatcccaagccctgccgacgatcgatgttcttgatgctatgtaaggccaaccctctccagaaagacatagtttgtagaggagattttcataagggttcctttcccctggcgtgtcagagacaaacattcccaaagaacgcttgactttcaaggcagccttcaaaattccttccaaattggattttgttactttgatggtctccagcatgtttccgccgtctattagacaagcaccagctttcaccgcagctgacaggctaaaattgtaccctgatatgtttatggcacttttcttgggctcaatgatccccaagattgggtgggtctgagagagtttgtctaagtcagacatgtttggatactttgcagtgtacacaagccccaagtctgacaacgattggatcacatcattcagatctgcctgcccttgtttgcacatgcaagcaatcgtcaggcttggcattgtcccaaactgattgtttaaaagctctgggtttcgaacatcccacactctaacaatgccatctccgagagtgtttcctgcccggaacccgccacccattccgaccatctgtaacaaaaccctcctctgttctagctgctgagctgttaggttgcccatatagactccagcagcaagaggcctctcacctctgatgacttttgctttgagtctgtccaggtcggcagcaaggacgaggaggtcatcagaggttagtgtccccactctcaaaacattcttctgttggactgactttaactcaactagattgttcactgcctggtttaggtccctcaatcttttcaggtcagagtcatccctcttctcctttctcatcaacctttgaacattggcaacttcagagaagtccagcccatgaagaagtgcttgagcatccttgatgacttggatctttatgttggagcagtaccctgagagttctctcctcaggctctgtgtccacaagaaggacttcacctcctttgaattggacat From 1ec21d98b91e49db83443f22b6f3e3fc0ec46c0c Mon Sep 17 00:00:00 2001 From: Jennifer Chang Date: Thu, 27 Feb 2025 18:20:47 -0800 Subject: [PATCH 2/7] Phylogenetic: Use outgroup for rooting the tree --- phylogenetic/defaults/config.yaml | 8 +++---- phylogenetic/rules/construct_phylogeny.smk | 27 +++++++++++++++++++--- 2 files changed, 28 insertions(+), 7 deletions(-) diff --git a/phylogenetic/defaults/config.yaml b/phylogenetic/defaults/config.yaml index 798761d..771bb96 100644 --- a/phylogenetic/defaults/config.yaml +++ b/phylogenetic/defaults/config.yaml @@ -33,10 +33,10 @@ refine: date_inference: "marginal" literature_clock_rate: 0.00078 #Ehichioya et al. 2019 # Root the tree based on "mid_point" for treetime - root: - l: "mid_point" - s: "mid_point" - gpc: "mid_point" + outgroup: + l: "NC_006574" + s: "NC_006575" + gpc: "NC_006575" ancestral: inference: "joint" diff --git a/phylogenetic/rules/construct_phylogeny.smk b/phylogenetic/rules/construct_phylogeny.smk index 83cda7c..f6dcdb9 100644 --- a/phylogenetic/rules/construct_phylogeny.smk +++ b/phylogenetic/rules/construct_phylogeny.smk @@ -19,10 +19,30 @@ This part of the workflow usually includes the following steps: See Augur's usage docs for these commands for more details. """ +rule add_outgroup: + """Add outgroup""" + input: + alignment = "results/{segment}/aligned.fasta", + outgroup = "defaults/{segment}/outgroup.fasta", + output: + alignment_with_outgroup = "results/{segment}/aligned_with_outgroup.fasta", + log: + "logs/{segment}/add-outgroup.txt", + benchmark: + "benchmarks/{segment}/add-outgroup.txt", + shell: + """ + augur align \ + --sequences {input.outgroup} \ + --existing-alignment {input.alignment} \ + --output {output.alignment_with_outgroup} \ + 2>&1 | tee {log} + """ + rule tree: """Building tree""" input: - alignment = "results/{segment}/aligned.fasta" + alignment = "results/{segment}/aligned_with_outgroup.fasta" output: tree = "results/{segment}/tree_raw.nwk" log: @@ -64,7 +84,7 @@ rule refine: coalescent = config['refine']['coalescent'], date_inference = config['refine']['date_inference'], literature_clock_rate = config['refine']['literature_clock_rate'], - root = lambda wildcards: config['refine']['root'][wildcards.segment], + outgroup = lambda wildcards: config['refine']['outgroup'][wildcards.segment], shell: """ augur refine \ @@ -78,7 +98,8 @@ rule refine: --coalescent {params.coalescent} \ --date-confidence \ --date-inference {params.date_inference} \ - --root {params.root} \ + --root {params.outgroup} \ + --remove-outgroup \ --clock-rate {params.literature_clock_rate} \ 2>&1 | tee {log} """ From 37bc3ed10be7fec3631149a58d1baff6a065f927 Mon Sep 17 00:00:00 2001 From: Jennifer Chang Date: Thu, 27 Feb 2025 18:21:58 -0800 Subject: [PATCH 3/7] Nextclade: Use outgroup for rooting the tree --- nextclade/defaults/config.yaml | 2 +- nextclade/rules/construct_phylogeny.smk | 25 +++++++++++++++++++++++-- nextclade_data/tree.json | 2 +- 3 files changed, 25 insertions(+), 4 deletions(-) diff --git a/nextclade/defaults/config.yaml b/nextclade/defaults/config.yaml index 360a868..0d769a5 100644 --- a/nextclade/defaults/config.yaml +++ b/nextclade/defaults/config.yaml @@ -14,7 +14,7 @@ refine: coalescent: "opt" date_inference: "marginal" clock_rate: 0.0006 - root: "mid_point" + outgroup: "NC_006575" ancestral: inference: "joint" diff --git a/nextclade/rules/construct_phylogeny.smk b/nextclade/rules/construct_phylogeny.smk index 00d678b..b985e6c 100644 --- a/nextclade/rules/construct_phylogeny.smk +++ b/nextclade/rules/construct_phylogeny.smk @@ -19,10 +19,30 @@ This part of the workflow usually includes the following steps: See Augur's usage docs for these commands for more details. """ +rule add_outgroup: + """Add outgroup""" + input: + alignment = "data/sequences.fasta", + outgroup = "../phylogenetic/defaults/gpc/outgroup.fasta", + output: + alignment_with_outgroup = "results/sequences_with_outgroup.fasta", + log: + "logs/add-outgroup.txt", + benchmark: + "benchmarks/add-outgroup.txt", + shell: + """ + augur align \ + --sequences {input.outgroup} \ + --existing-alignment {input.alignment} \ + --output {output.alignment_with_outgroup} \ + 2>&1 | tee {log} + """ + rule tree: """Building tree""" input: - alignment = "data/sequences.fasta" + alignment = "results/sequences_with_outgroup.fasta" output: tree = "results/tree_raw.nwk" log: @@ -64,7 +84,7 @@ rule refine: coalescent = config['refine']['coalescent'], date_inference = config['refine']['date_inference'], clock_rate = config['refine']['clock_rate'], - root = lambda wildcards: config['refine']['root'], + root = lambda wildcards: config['refine']['outgroup'], shell: """ augur refine \ @@ -80,5 +100,6 @@ rule refine: --date-confidence \ --date-inference {params.date_inference} \ --root {params.root} \ + --remove-outgroup \ 2>&1 | tee {log} """ diff --git a/nextclade_data/tree.json b/nextclade_data/tree.json index 15b64f3..2be1a70 100644 --- a/nextclade_data/tree.json +++ b/nextclade_data/tree.json @@ -1 +1 @@ -{"version": "v2", "meta": {"title": "Real-time tracking of Lassa virus evolution", "updated": "2025-02-05", "build_url": "https://github.com/nextstrain/lassa", "data_provenance": [{"name": "GenBank", "url": "https://www.ncbi.nlm.nih.gov/genbank/"}], "maintainers": [{"name": "Jennifer Chang", "url": "https://bedford.io/team/jennifer-chang/"}, {"name": "Richard Daodu", "url": "https://github.com/JoiRichi"}, {"name": "Denise K\u00fchnert", "url": "https://www.shh.mpg.de/person/54587/935000"}, {"name": "the Nextstrain team", "url": "https://nextstrain.org/team"}], "display_defaults": {"map_triplicate": false, "color_by": "clade_membership", "distance_measure": "div"}, "genome_annotations": {"nuc": {"end": 1476, "start": 1, "strand": "+", "type": "source", "seqid": "../phylogenetic/defaults/lassa_gpc.gb"}, "GPC": {"end": 1476, "seqid": "../phylogenetic/defaults/lassa_gpc.gb", "start": 1, "strand": "+", "type": "CDS"}}, "description": "We gratefully acknowledge the authors, originating and submitting laboratories of the genetic sequences and metadata for sharing their work.\n\nSpecial thanks to Richard Daodu and Laura McMullan for comments, code and suggestions.\n\nPlease note that although data generators have generously shared data in an open fashion, that does not mean there should be free license to publish on this data. Data generators should be cited where possible and collaborations should be sought in some circumstances. Please try to avoid scooping someone else's work. Reach out if uncertain.\n\nMuch of the genomic data here comes from publications [Andersen et al 2015](https://doi.org/10.1016/j.cell.2015.07.020), [Siddle et al 2018](https://doi.org/10.1056/NEJMoa1804498\n) and [Kafetzopoulou et al 2019](https://doi.org/10.1126/science.aau9343), but with more recent sequences from NCBI may not yet be published.\n\nWe maintain two views of Lassa virus evolution: one showing evolution of the [L segment](https://nextstrain.org/lassa/l) and the other showing evolution of the [S segment](https://nextstrain.org/lassa/s). A tangle tree showing [co-evolution of L and S](https://nextstrain.org/lassa/l:lassa/s) is also available.\n\n#### Underlying data\n\nWe curate sequence data and metadata from NCBI as the starting point for our analyses. Curated sequences and metadata are available as flat files at:\n\n##### L segment\n* [data.nextstrain.org/files/workflows/lassa/l/sequences.fasta.zst](https://data.nextstrain.org/files/workflows/lassa/l/sequences.fasta.zst)\n* [data.nextstrain.org/files/workflows/lassa/l/metadata.tsv.zst](https://data.nextstrain.org/files/workflows/lassa/l/metadata.tsv.zst)\n\n##### S segment\n* [data.nextstrain.org/files/workflows/lassa/s/sequences.fasta.zst](https://data.nextstrain.org/files/workflows/lassa/s/sequences.fasta.zst)\n* [data.nextstrain.org/files/workflows/lassa/s/metadata.tsv.zst](https://data.nextstrain.org/files/workflows/lassa/s/metadata.tsv.zst)\n\n##### Both segments combined\n* [data.nextstrain.org/files/workflows/lassa/all/sequences.fasta.zst](https://data.nextstrain.org/files/workflows/lassa/all/sequences.fasta.zst)\n* [data.nextstrain.org/files/workflows/lassa/all/metadata.tsv.zst](https://data.nextstrain.org/files/workflows/lassa/all/metadata.tsv.zst)\n\n---\n\nScreenshots may be used under a [CC-BY-4.0 license](https://creativecommons.org/licenses/by/4.0/) and attribution to nextstrain.org must be provided.\n", "colorings": [{"key": "gt", "title": "Genotype", "type": "categorical"}, {"key": "num_date", "title": "Date", "type": "continuous"}, {"key": "country", "title": "Country", "type": "categorical", "scale": [["Sierra Leone", "#4068CF"], ["Guinea", "#5098B9"], ["Liberia", "#6CB28C"], ["C\u00f4te d'Ivoire", "#94BD62"], ["Mali", "#BFBB47"], ["Togo", "#DFA53B"], ["Benin", "#E67131"], ["Nigeria", "#DB2823"]]}, {"key": "division", "title": "Admin Division", "type": "categorical"}, {"key": "host", "title": "Host", "type": "categorical", "scale": [["Homo sapiens", "#4A8CC2"], ["Mastomys", "#71B486"], ["Mastomys erythroleucus", "#ABBD52"], ["Mastomys natalensis", "#DEA73C"]]}, {"key": "abbr_authors", "title": "Authors", "type": "categorical"}, {"key": "clade_membership", "title": "Clade", "type": "categorical"}], "filters": ["country", "division", "host", "abbr_authors", "clade_membership", "lineage_name"], "geo_resolutions": [{"key": "country", "demes": {"Nigeria": {"latitude": 10.0, "longitude": 8.0}, "Benin": {"latitude": 9.961027, "longitude": 2.327362}, "Mali": {"latitude": 16.3700359, "longitude": -2.2900239}, "C\u00f4te d'Ivoire": {"latitude": 7.9897371, "longitude": -5.5679458}, "Sierra Leone": {"latitude": 8.6400349, "longitude": -11.8400269}, "Guinea": {"latitude": 10.7226226, "longitude": -10.7083587}, "Liberia": {"latitude": 5.7499721, "longitude": -9.3658524}, "Togo": {"latitude": 8.88625, "longitude": 1.069709}}}], "panels": ["tree", "map", "entropy"], "extensions": {"clade_node_attrs": [{"name": "lineage_name", "displayName": "Lassa lineage name", "description": "Global lassa lineages based on [citation here]."}], "nextclade": {"pathogen": {"schemaVersion": "3.0.0", "defaultCds": "GPC", "attributes": {"name": "Lassa Global Tree", "reference name": "Josiah", "reference accession": "NC_004296"}, "alignmentParams": {"penaltyGapExtend": 1, "penaltyGapOpen": 8, "penaltyGapOpenInFrame": 9, "penaltyGapOpenOutOfFrame": 10, "penaltyMismatch": 1, "scoreMatch": 5, "retryReverseComplement": true, "allowedMismatches": 10, "minSeedCover": 0.01}, "qc": {"missingData": {"enabled": true, "missingDataThreshold": 20, "scoreBias": 4}, "mixedSites": {"enabled": true, "mixedSitesThreshold": 4}, "frameShifts": {"enabled": true}, "stopCodons": {"enabled": true}, "privateMutations": {"enabled": true, "cutoff": 12, "typical": 4, "weightLabeledSubstitutions": 1, "weightReversionSubstitutions": 1, "weightUnlabeledSubstitutions": 1}, "snpClusters": {"enabled": true, "clusterCutOff": 3, "scoreWeight": 50, "windowSize": 50}}}}}}, "tree": {"name": "NODE_0000000", "node_attrs": {"div": 0, "num_date": {"value": 1647.737, "confidence": [1636.32, 1662.569]}, "clade_membership": {"value": "LIII", "confidence": {"LIII": 0.33, "LII": 0.243, "LIV_V": 0.225, "LVII": 0.104, "LI": 0.0987}, "entropy": 1.509}}, "branch_attrs": {"mutations": {"nuc": ["A6G", "A9G", "G13A", "G15A", "C24T", "G27A", "A42T", "A48G", "T66C", "C69A", "G78C", "T81C", "G82C", "A84C", "A87G", "G91A", "G93C", "A99G", "T102G", "C103A", "T112G", "A117T", "G120A", "T129C", "G130A", "T135C", "T136C", "T144C", "C150T", "C151T", "G153C", "T154C", "T162A", "G165A", "T168A", "A172T", "C177G", "A178-", "G179-", "T180-", "C181A", "T183C", "T186C", "G201A", "T204A", "G207A", "T210C", "G213A", "A216G", "A219G", "A231C", "T237C", "T249C", "C252A", "T273C", "T276C", "T282C", "T287G", "A306C", "A309G", "A312G", "C318T", "G321A", "G330A", "T336C", "T339C", "A348G", "T351C", "T357C", "G360T", "C369T", "A375G", "C381T", "C384T", "T399C", "A408C", "C423T", "T424C", "C432T", "C435A", "C462T", "C465T", "T468C", "T471C", "A480G", "G483A", "T486C", "C501T", "G504C", "A511G", "G512C", "C513T", "T537C", "T543C", "T546A", "T562C", "A564G", "T573C", "G594A", "C597T", "T606A", "A615T", "C624G", "T639A", "T645C", "A654G", "T657C", "C658T", "C666T", "A669G", "T672C", "C678T", "C693T", "G702A", "C714T", "C717T", "C726T", "C732A", "C735G", "G744A", "T753C", "T759C", "T762C", "A768G", "T772C", "A789C", "T804C", "A810G", "T813C", "A816T", "C819A", "G828A", "A831T", "T834C", "G840A", "A855G", "A870G", "A873G", "C876T", "C879T", "T903C", "T927C", "A960G", "T969C", "A972G", "G978A", "A981G", "A987G", "T1002C", "G1005A", "T1006C", "A1023G", "T1030C", "G1032A", "A1044G", "T1047G", "A1050C", "C1063T", "A1065G", "C1066A", "A1080G", "T1083A", "T1092C", "C1113T", "C1119T", "T1131A", "C1149A", "T1155C", "T1173A", "A1176C", "T1180C", "C1185T", "G1188A", "T1206C", "T1221A", "T1227C", "C1233A", "T1236A", "G1239A", "T1243C", "A1245G", "G1248A", "G1254A", "T1257C", "G1263T", "G1266A", "G1269A", "A1281T", "T1287A", "C1299T", "G1305C", "T1311C", "C1320T", "T1326C", "T1329C", "C1335T", "T1341C", "C1345T", "A1347G", "G1368A", "T1371C", "A1377G", "C1380A", "G1383A", "T1384C", "G1386A", "T1389C", "T1398C", "T1405C", "G1407C", "T1410C", "T1413C", "T1425C", "C1428T", "A1434T", "C1437G", "G1455C", "T1458A", "G1461C", "A1463G", "G1475A"], "GPC": ["V5I", "V28L", "V31I", "L35M", "F38V", "V44I", "L51F", "T58S", "S60-", "L61I", "M96R", "S171A", "K272N", "D273E", "E421D", "S462P", "K488R"]}, "labels": {"aa": "GPC: V5I, V28L, V31I, L35M, F38V, V44I, L51F, T58S, S60-, L61I, M96R, S171A, K272N, D273E, E421D, S462P, K488R"}}, "children": [{"name": "NODE_0000001", "node_attrs": {"div": 0.0118, "num_date": {"value": 1669.101, "confidence": [1660.468, 1681.848]}, "clade_membership": {"value": "LII", "confidence": {"LII": 0.315, "LIII": 0.254, "LIV_V": 0.172, "LVII": 0.133, "LI": 0.127}, "entropy": 1.545}}, "branch_attrs": {"mutations": {"nuc": ["C135G", "A201G", "C250T", "C543G", "C618A", "C619A", "T621G", "T648C", "A828T", "C1011A", "T1029A", "A1125T", "G1275A", "T1422A"]}}, "children": [{"name": "NODE_0000002", "node_attrs": {"div": 0.0568, "num_date": {"value": 1740.182, "confidence": [1729.285, 1755.881]}, "clade_membership": {"value": "LVII", "confidence": {"LVII": 0.293, "LI": 0.276, "LII": 0.185, "LIII": 0.147, "LIV_V": 0.0989}, "entropy": 1.538}}, "branch_attrs": {"mutations": {"nuc": ["C126G", "C127A", "A168T", "C171T", "A175C", "C176T", "T194G", "A204G", "C211T", "C217T", "G219A", "C222T", "C234A", "C255A", "A261T", "G288A", "A303T", "C307T", "A330C", "C339A", "G348A", "T360A", "G375A", "T417A", "G477A", "G495A", "C510T", "A532G", "C534A", "T570A", "T678A", "T693C", "G729C", "C733T", "T747A", "C759T", "A771G", "A777G", "C838T", "C943T", "C966A", "C1006T", "G1008A", "C1014T", "C1030T", "C1041T", "G1080C", "A1167C", "C1179T", "G1260C", "C1341A", "G1348A", "A1359T", "G1377T", "C1419A", "T1434A", "G1459A", "T1460C"], "GPC": ["L43I", "T59L", "V65G", "N178E", "M420I", "V450I", "V487T"]}, "labels": {"aa": "GPC: L43I, T59L, V65G, N178E, M420I, V450I, V487T"}}, "children": [{"name": "Pinneo-NIG-1969", "node_attrs": {"div": 0.201, "num_date": {"value": 1969.999, "confidence": [1969.101, 1969.999]}, "accession": "KM822128", "author": {"author": "Andersen,K.G.,Shapiro,B.J.,Matranga,C.B.,Gire,S.K.,Sealfon,R.,England,E.M.,Winnicki,S.,Moses,L.M.,Stremlau,M.,Folarin,O.,Odia,I.,Ehiane,P.,Goba,A.,Momoh,M.,Gnirke,A.,Birren,B.,Hensley,L.,Levin,J.Z.,Happi,C.T.,Garry,R.F.,Sabeti,P.C.", "value": "Andersen,K.G.,Shapiro,B.J.,Matranga,C.B.,Gire,S.K.,Sealfon,R.,England,E.M.,Winnicki,S.,Moses,L.M.,Stremlau,M.,Folarin,O.,Odia,I.,Ehiane,P.,Goba,A.,Momoh,M.,Gnirke,A.,Birren,B.,Hensley,L.,Levin,J.Z.,Happi,C.T.,Garry,R.F.,Sabeti,P.C."}, "country": {"value": "Nigeria"}, "abbr_authors": {"value": "Andersen et al."}, "clade_membership": {"value": "LI", "confidence": {"LI": 1.0}, "entropy": -1e-12}, "genbank_accession": {"value": "KM822128"}}, "branch_attrs": {"mutations": {"nuc": ["A12T", "A15T", "T36A", "T42A", "G51A", "G54C", "C66G", "A75G", "C78T", "C81T", "C84A", "C85T", "C94T", "G102C", "A103T", "C108T", "T111C", "G112A", "T114C", "C129T", "G135A", "C136T", "C141T", "A142G", "C147T", "C148T", "T150A", "C154T", "A162C", "G164A", "A165G", "A174C", "G177A", "T182C", "T184C", "A185T", "C186T", "T195A", "G216A", "T261C", "A269G", "C273T", "C276T", "C306A", "G309A", "G312A", "C313T", "C324T", "C336T", "C351T", "C358T", "T363C", "C390T", "C393T", "G426A", "G453A", "A456C", "C468T", "T501C", "A505T", "G506C", "G511T", "T513C", "A528G", "A552C", "T555C", "T558A", "C562T", "G567A", "C573T", "G579A", "T585C", "T597A", "C607T", "T609A", "T615A", "G620A", "G624A", "T651C", "T658C", "G669A", "C672T", "A684G", "T687C", "A708G", "T717C", "T720G", "T723C", "A732T", "A744G", "C753T", "T756A", "C762A", "G774C", "C775T", "C780G", "A783C", "C796T", "C804T", "C834T", "G855A", "G861A", "T864A", "G870C", "C885T", "A924G", "C927T", "G942A", "C951T", "A971G", "G972T", "A978G", "A990C", "A993G", "C999T", "C1002T", "A1020C", "A1029C", "A1035C", "G1044A", "C1045T", "G1047A", "G1065A", "G1068A", "A1083T", "A1086C", "T1113C", "C1116T", "C1122T", "C1127G", "C1130G", "A1131C", "G1146A", "A1152G", "C1155T", "G1162A", "A1173G", 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"ATGGGACAAATAGTGACATTCTTCCAGGAAGTGCCTCATGTAATAGAAGAGGTGATGAACATTGTTCTCATTGCACTGTCTGTACTAGCAGTGCTGAAAGGTCTGTACAATTTTGCAACGTGTGGCCTTGTTGGTTTGGTCACTTTCCTCCTGTTGTGTGGTAGGTCTTGCACAACCAGTCTTTATAAAGGGGTTTATGAGCTTCAGACTCTGGAACTAAACATGGAGACACTCAATATGACCATGCCTCTCTCCTGCACAAAGAACAACAGTCATCATTATATAATGGTGGGCAATGAGACAGGACTAGAACTGACCTTGACCAACACGAGCATTATTAATCACAAATTTTGCAATCTGTCTGATGCCCACAAAAAGAACCTCTATGACCACGCTCTTATGAGCATAATCTCAACTTTCCACTTGTCCATCCCCAACTTCAATCAGTATGAGGCAATGAGCTGCGATTTTAATGGGGGAAAGATTAGTGTGCAGTACAACCTGAGTCACAGCTATGCTGGGGATGCAGCCAACCATTGTGGTACTGTTGCAAATGGTGTGTTACAGACTTTTATGAGGATGGCTTGGGGTGGGAGCTACATTGCTCTTGACTCAGGCCGTGGCAACTGGGACTGTATTATGACTAGTTATCAATATCTGATAATCCAAAATACAACCTGGGAAGATCACTGCCAATTCTCGAGACCATCTCCCATCGGTTATCTCGGGCTCCTCTCACAAAGGACTAGAGATATTTATATTAGTAGAAGATTGCTAGGCACATTCACATGGACACTGTCAGATTCTGAAGGTAAAGACACACCAGGGGGATATTGTCTGACCAGGTGGATGCTAATTGAGGCTGAACTAAAATGCTTCGGGAACACAGCTGTGGCAAAATGTAATGAGAAGCATGATGAGGAATTTTGTGACATGCTGAGGCTGTTTGACTTCAACAAACAAGCCATTCAAAGGTTGAAAGCTGAAGCACAAATGAGCATTCAGTTGATCAACAAAGCAGTAAATGCTTTGATAAATGACCAACTTATAATGAAGAACCATCTACGGGACATCATGGGAATTCCATACTGTAATTACAGCAAGTATTGGTACCTCAACCACACAACTACTGGGAGAACATCACTGCCCAAATGTTGGCTTGTATCAAATGGTTCATACTTGAACGAGACCCACTTTTCTGATGATATTGAACAACAAGCTGACAATATGATCACTGAGATGTTACAGAAGGAGTATATGGAGAGGCAGGGGAAGACACCATTGGGTCTAGTTGACCTCTTTGTGTTCAGTACAAGTTTCTATCTTATTAGCATCTTCCTTCACCTAGTCAAAATACCAACTCATAGGCATATTGTAGGCAAGTCGTGTCCCAAACCTCACAGATTGAATCATATGGGCATTTGTTCCTGTGGACTCTACAAACAGCCTGGTGTGCCTGTGAAATGGAAGAGATGA", "GPC": "MGQIVTFFQEVPHVIEEVMNIVLIALSVLAVLKGLYNFATCGLVGLVTFLLLCGRSCTTSLYKGVYELQTLELNMETLNMTMPLSCTKNNSHHYIMVGNETGLELTLTNTSIINHKFCNLSDAHKKNLYDHALMSIISTFHLSIPNFNQYEAMSCDFNGGKISVQYNLSHSYAGDAANHCGTVANGVLQTFMRMAWGGSYIALDSGRGNWDCIMTSYQYLIIQNTTWEDHCQFSRPSPIGYLGLLSQRTRDIYISRRLLGTFTWTLSDSEGKDTPGGYCLTRWMLIEAELKCFGNTAVAKCNEKHDEEFCDMLRLFDFNKQAIQRLKAEAQMSIQLINKAVNALINDQLIMKNHLRDIMGIPYCNYSKYWYLNHTTTGRTSLPKCWLVSNGSYLNETHFSDDIEQQADNMITEMLQKEYMERQGKTPLGLVDLFVFSTSFYLISIFLHLVKIPTHRHIVGKSCPKPHRLNHMGICSCGLYKQPGVPVKWKR*"}} \ No newline at end of file +{"version": "v2", "meta": {"title": "Real-time tracking of Lassa virus evolution", "updated": "2025-02-27", "build_url": "https://github.com/nextstrain/lassa", "data_provenance": [{"name": "GenBank", "url": "https://www.ncbi.nlm.nih.gov/genbank/"}], "maintainers": [{"name": "Jennifer Chang", "url": "https://bedford.io/team/jennifer-chang/"}, {"name": "Richard Daodu", "url": "https://github.com/JoiRichi"}, {"name": "Denise K\u00fchnert", "url": "https://www.shh.mpg.de/person/54587/935000"}, {"name": "the Nextstrain team", "url": "https://nextstrain.org/team"}], "display_defaults": {"map_triplicate": false, "color_by": "clade_membership", "distance_measure": "div"}, "genome_annotations": {"nuc": {"end": 1476, "start": 1, "strand": "+", "type": "source", "seqid": "../phylogenetic/defaults/lassa_gpc.gb"}, "GPC": {"end": 1476, "seqid": "../phylogenetic/defaults/lassa_gpc.gb", "start": 1, "strand": "+", "type": "CDS"}}, "description": "We gratefully acknowledge the authors, originating and submitting laboratories of the genetic sequences and metadata for sharing their work.\n\nSpecial thanks to Richard Daodu and Laura McMullan for comments, code and suggestions.\n\nPlease note that although data generators have generously shared data in an open fashion, that does not mean there should be free license to publish on this data. Data generators should be cited where possible and collaborations should be sought in some circumstances. Please try to avoid scooping someone else's work. Reach out if uncertain.\n\nMuch of the genomic data here comes from publications [Andersen et al 2015](https://doi.org/10.1016/j.cell.2015.07.020), [Siddle et al 2018](https://doi.org/10.1056/NEJMoa1804498\n) and [Kafetzopoulou et al 2019](https://doi.org/10.1126/science.aau9343), but with more recent sequences from NCBI may not yet be published.\n\nWe maintain two views of Lassa virus evolution: one showing evolution of the [L segment](https://nextstrain.org/lassa/l) and the other showing evolution of the [S segment](https://nextstrain.org/lassa/s). A tangle tree showing [co-evolution of L and S](https://nextstrain.org/lassa/l:lassa/s) is also available.\n\n#### Underlying data\n\nWe curate sequence data and metadata from NCBI as the starting point for our analyses. Curated sequences and metadata are available as flat files at:\n\n##### L segment\n* [data.nextstrain.org/files/workflows/lassa/l/sequences.fasta.zst](https://data.nextstrain.org/files/workflows/lassa/l/sequences.fasta.zst)\n* [data.nextstrain.org/files/workflows/lassa/l/metadata.tsv.zst](https://data.nextstrain.org/files/workflows/lassa/l/metadata.tsv.zst)\n\n##### S segment\n* [data.nextstrain.org/files/workflows/lassa/s/sequences.fasta.zst](https://data.nextstrain.org/files/workflows/lassa/s/sequences.fasta.zst)\n* [data.nextstrain.org/files/workflows/lassa/s/metadata.tsv.zst](https://data.nextstrain.org/files/workflows/lassa/s/metadata.tsv.zst)\n\n##### Both segments combined\n* [data.nextstrain.org/files/workflows/lassa/all/sequences.fasta.zst](https://data.nextstrain.org/files/workflows/lassa/all/sequences.fasta.zst)\n* [data.nextstrain.org/files/workflows/lassa/all/metadata.tsv.zst](https://data.nextstrain.org/files/workflows/lassa/all/metadata.tsv.zst)\n\n---\n\nScreenshots may be used under a [CC-BY-4.0 license](https://creativecommons.org/licenses/by/4.0/) and attribution to nextstrain.org must be provided.\n", "colorings": [{"key": "gt", "title": "Genotype", "type": "categorical"}, {"key": "num_date", "title": "Date", "type": "continuous"}, {"key": "country", "title": "Country", "type": "categorical", "scale": [["Sierra Leone", "#4068CF"], ["Guinea", "#5098B9"], ["Liberia", "#6CB28C"], ["C\u00f4te d'Ivoire", "#94BD62"], ["Mali", "#BFBB47"], ["Togo", "#DFA53B"], ["Benin", "#E67131"], ["Nigeria", "#DB2823"]]}, {"key": "division", "title": "Admin Division", "type": "categorical"}, {"key": "host", "title": "Host", "type": "categorical", "scale": [["Homo sapiens", "#4A8CC2"], ["Mastomys", "#71B486"], ["Mastomys erythroleucus", "#ABBD52"], ["Mastomys natalensis", "#DEA73C"]]}, {"key": "abbr_authors", "title": "Authors", "type": "categorical"}, {"key": "clade_membership", "title": "Clade", "type": "categorical"}], "filters": ["country", "division", "host", "abbr_authors", "clade_membership", "lineage_name"], "geo_resolutions": [{"key": "country", "demes": {"Guinea": {"latitude": 10.7226226, "longitude": -10.7083587}, "Liberia": {"latitude": 5.7499721, "longitude": -9.3658524}, "Nigeria": {"latitude": 10.0, "longitude": 8.0}, "C\u00f4te d'Ivoire": {"latitude": 7.9897371, "longitude": -5.5679458}, "Sierra Leone": {"latitude": 8.6400349, "longitude": -11.8400269}, "Benin": {"latitude": 9.961027, "longitude": 2.327362}, "Mali": {"latitude": 16.3700359, "longitude": -2.2900239}, "Togo": {"latitude": 8.88625, "longitude": 1.069709}}}], "panels": ["tree", "map", "entropy"], "extensions": {"clade_node_attrs": [{"name": "lineage_name", "displayName": "Lassa lineage name", "description": "Global lassa lineages based on [citation here]."}], "nextclade": {"pathogen": {"schemaVersion": "3.0.0", "defaultCds": "GPC", "attributes": {"name": "Lassa Global Tree", "reference name": "Josiah", "reference accession": "NC_004296"}, "alignmentParams": {"penaltyGapExtend": 1, "penaltyGapOpen": 8, "penaltyGapOpenInFrame": 9, "penaltyGapOpenOutOfFrame": 10, "penaltyMismatch": 1, "scoreMatch": 5, "retryReverseComplement": true, "allowedMismatches": 10, "minSeedCover": 0.01}, "qc": {"missingData": {"enabled": true, "missingDataThreshold": 20, "scoreBias": 4}, "mixedSites": {"enabled": true, "mixedSitesThreshold": 4}, "frameShifts": {"enabled": true}, "stopCodons": {"enabled": true}, "privateMutations": {"enabled": true, "cutoff": 12, "typical": 4, "weightLabeledSubstitutions": 1, "weightReversionSubstitutions": 1, "weightUnlabeledSubstitutions": 1}, "snpClusters": {"enabled": true, "clusterCutOff": 3, "scoreWeight": 50, "windowSize": 50}}}}}}, "tree": {"name": "NODE_0000000", "node_attrs": {"div": 0, "num_date": {"value": 1634.001, "confidence": [1625.527, 1647.293]}, "clade_membership": {"value": "LII", "confidence": {"LII": 0.372, "LIII": 0.251, "LIV_V": 0.186, "LVII": 0.0981, "LI": 0.0932}, "entropy": 1.477}}, "branch_attrs": {"mutations": {"nuc": ["A6G", "A9G", "A12T", "G13A", "C24T", "G27A", "A42T", "A48G", "G51A", "T66C", "C69A", "C76T", "G78C", "G82C", "A87G", "G91A", "G93A", "A99G", "T102G", "C103A", "G105C", "T111C", "T112A", "A117C", "G120A", "T129C", "G130A", "T135A", "T136C", "T144C", "C150T", "G153C", "T154C", "T162A", "G165A", "T168C", "A172T", "C177A", "A178-", "G179-", "T180-", "C181A", "T183C", "T186C", "T204A", "G207A", "T210C", "C211T", "A219G", "A220G", "C230A", "A231C", "T237C", "C243T", "T249C", "C250T", "C252A", "T276C", "T282C", "A285C", "T287G", "A306C", "C307T", "A309G", "C318T", "G321A", "C327T", "G330A", "T336C", "T339C", "A348G", "T351C", "T357C", "G360T", "C369T", "A375G", "C381T", "T399C", "A408C", "T424C", "C432T", "C435A", "C462T", "C465T", "T468C", "T471C", "A480G", "G483A", "T486A", "C501T", "G504C", "A511G", "G512C", "C513T", "T537C", "T543G", "T546A", "A564G", "T570C", "T573C", "G594A", "C597T", "T606A", "A615T", "C618A", "C619A", "G620A", "T621G", "C624G", "C633T", "T639A", "T645C", "T648C", "A654G", "T657C", "C658T", "C666T", "A669G", "T672C", "C678T", "G702A", "A703C", "C714T", "C717T", "C726T", "G729A", "C732A", "C733T", "C735G", "A741G", "G744A", "T747C", "T753C", "A766C", "A768G", "T772C", "C780A", "A789C", "G798C", "A801T", "T804C", "A810G", "T813C", "A816T", "C819A", "G828T", "A831T", "T834C", "G840A", "A855G", "G861A", "A870G", "A873G", "C879T", "T891A", "G894T", "T903C", "T927C", "G942A", "A960G", "A972G", "T976C", "G978A", "A981G", "A987G", "A993G", "T1002C", "G1005A", "T1006C", "C1011A", "A1023G", "T1029C", "G1032A", "A1044G", "T1047G", "A1050C", "C1063T", "C1066A", "A1080G", "T1083A", "T1092C", "C1119T", "A1125T", "A1126G", "C1127T", "T1128C", "T1131A", "G1136A", "C1149A", "T1155C", "T1173A", "T1180C", "C1185T", "G1188A", "T1206C", "T1221A", "T1227C", "C1233A", "T1236A", "G1239A", "T1243C", "G1248A", "G1254A", "T1257C", "G1263C", "G1269A", "G1275A", "A1281T", "G1284A", "T1287A", "C1299T", "G1305C", "T1311C", "A1314T", "C1320T", "T1326G", "T1329C", "C1335T", "T1341C", "C1345T", "A1347G", "A1353G", "G1368A", "T1371C", "A1377G", "C1380G", "G1383A", "T1384C", "G1386A", "T1389C", "T1398C", "T1405C", "G1407C", "T1410C", "T1413C", "T1422A", "T1425C", "C1428T", "A1434T", "C1437G", "G1446A", "G1455C", "T1458A", "G1461C", "G1470A", "G1475A"], "GPC": ["V5M", "L26F", "V28L", "V31I", "L35I", "F38I", "V44I", "T58S", "S60-", "L61I", "N74D", "T77N", "M96R", "S171A", "R207K", "K272N", "D273E", "T376V", "R379K", "E421D", "S462P"]}, "labels": {"aa": "GPC: V5M, L26F, V28L, V31I, L35I, F38I, V44I, T58S, S60-, L61I, N74D, T77N, M96R, S171A, R207K, K272N, D273E, T376V, R379K, E421D, S462P"}}, "children": [{"name": "NODE_0000001", "node_attrs": {"div": 0.0551, "num_date": {"value": 1773.564, "confidence": [1761.714, 1785.433]}, "clade_membership": {"value": "LII", "confidence": {"LII": 0.99, "LIII": 0.00381, "LIV_V": 0.00276, "LVII": 0.00165, "LI": 0.0016}, "entropy": 0.0681}}, "branch_attrs": {"mutations": {"nuc": ["G9A", "T12A", "G15A", "T42C", "T76C", "T79A", "C80G", "A84C", "C111T", "A112G", "A120C", "A130T", "G139A", "A142T", "C147T", "C168A", "G192T", "T195C", "C210T", "T211C", "A227C", "G228A", "T243A", "G287T", "G291T", "C294A", "C333T", "C393T", "C397T", "C399G", "T501C", "A546C", "G561C", "T562C", "A594C", "T603A", "C645T", "A646T", "G647C", "A675C", "C699T", "A702T", "A705C", "T711C", "T726G", "T762C", "G774C", "A777C", "A783T", "A795T", "C804T", "A825T", "T831G", "C937T", "T969A", "C970A", "T984A", "C1029A", "T1030C", "A1035C", "C1045T", "T1062C", "C1071T", "A1083T", "A1086T", "C1113T", "C1116A", "C1128G", "A1176T", "C1191A", "A1254G", "C1257T", "A1287G", "T1293G", "C1296T", "G1326C", "C1329T", "A1356C", "T1362C", "T1365C", "A1386C", "C1398A", "T1428A", "A1476G"], "GPC": ["M5I", "F26L", "I38V", "I44F", "V47I", "T48S", "E76A", "R96M", "Q324K"]}, "labels": {"aa": "GPC: M5I, F26L, I38V, I44F, V47I, T48S, E76A, R96M, Q324K"}}, "children": [{"name": "LASV/H.sapiens-tc/NGA/2012/IRR_006", "node_attrs": {"div": 0.167, "num_date": {"value": 2012.141, "confidence": [2012.141, 2012.141], "inferred": false}, "accession": "MK107967", "author": {"author": "Ehichioya,D.U.,Lemey,P.,Kafetzopoulou,L.E.,Rieger,T.,Cadar,D.,Duraffour,S.,Ogbaini-Emovon,E.,Okogbenin,S.,Asogun,D.,Gunther,S.", "value": "Ehichioya,D.U.,Lemey,P.,Kafetzopoulou,L.E.,Rieger,T.,Cadar,D.,Duraffour,S.,Ogbaini-Emovon,E.,Okogbenin,S.,Asogun,D.,Gunther,S."}, "host": {"value": "Homo sapiens"}, "division": {"value": "Rivers"}, "abbr_authors": {"value": "Ehichioya et al."}, "clade_membership": {"value": "LII", "confidence": {"LII": 1.0}, "entropy": -1e-12}, "country": {"value": "Nigeria"}, "genbank_accession": {"value": "MK107967"}}, "branch_attrs": {"mutations": {"nuc": ["A18T", "T39C", "G48A", "A69G", "C84T", "A93G", "G102A", "C117T", "C120T", "C126A", "G138A", "C144A", "C153T", "T159C", "A174G", "-178A", "-179C", "-180A", "A181C", "A189G", "T198C", "G213A", "C237T", "C249T", "C258T", "C267T", "C306T", "T307C", "C313T", "C339T", "C345T", "T363C", "C372T", "G388A", "G399A", "A414T", "C420T", "C429T", "T432C", "C438T", "C441T", "T444C", "A456T", "T465C", "T474C", "G492T", "T507C", "C510T", "C512G", "A528T", "C531G", "A532G", "C534G", "C537T", "C546T", "T558G", "C561T", "G564T", "G567A", "G579A", "T585C", "C594T", "C607T", "T609G", "A618G", "C648T", "T658C", "G660A", "A684G", "C693T", "C705T", "G726A", "A732G", "T733C", "C747T", "C777T", "A780C", "T783C", "C789T", "T795C", "C813A", "A819T", "A820G", "A822G", "C834T", "A840G", "A867G", "C868T", "G870A", "G882A", "C885T", "A891T", "G892A", "C903T", "G909A", "A942G", "G945C", "C957T", "A963G", "C966T", "G972A", "A978G", "G982A", "G1008C", "A1020G", "G1023T", "G1044A", "C1059T", "G1068A", "C1092T", "C1101T", "G1104A", "T1107C", "C1114T", "C1120A", "T1125G", "A1137G", "A1138T", "C1144T", "G1146A", "A1149G", "A1164T", "C1179T", "T1203A", "C1206T", "C1227T", "G1260A", "C1263T", "G1266A", "G1272A", "T1282C", "A1290T", "C1297A", "G1303A", "C1308T", "T1314C", "C1326T", "G1353A", "C1356T", "A1359G", "G1375A", "T1376C", "G1377A", "C1386T", "T1434C", "G1437A", "T1449C", "C1455T", "A1458T", "C1461T"], "GPC": ["I31M", "-60T", "I61L", "D130N", "A171G", "N178E", "E273D", "T274A", "V298I", "A328T", "H374N", "T380S", "D401E", "M420I", "L433I", "V435I", "V459T"]}, "labels": {"aa": "GPC: I31M, -60T, I61L, D130N, A171G, N178E, E273D, T274A, V298I, A328T, H374N, T380S, D401E, M420I, L433I, V435I, V459T"}}}, {"name": "NODE_0000002", "node_attrs": {"div": 0.0774, "num_date": {"value": 1818.703, "confidence": [1808.504, 1832.094]}, "clade_membership": {"value": "LII", "confidence": {"LII": 1.0}, "entropy": 0.00242}}, "branch_attrs": {"mutations": {"nuc": ["A27G", "A51G", "A75C", "C105T", "T182C", "A216G", "T273C", "C324A", "T369A", "C424T", "G453A", "G547A", "A552C", "C570T", "G669A", "T759C", "C843T", "G846A", "A897G", "G960A", "A1173T", "C1194T", "A1240C", "C1243T", "A1245G", "T1281C", "C1288T", "T1317C", "A1395G", "A1446T"], "GPC": ["I61T", "V183I", "M414L", 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"Andersen,K.G.,Shapiro,B.J.,Matranga,C.B.,Gire,S.K.,Sealfon,R.,England,E.M.,Winnicki,S.,Moses,L.M.,Stremlau,M.,Folarin,O.,Odia,I.,Ehiane,P.,Goba,A.,Momoh,M.,Gnirke,A.,Birren,B.,Hensley,L.,Levin,J.Z.,Happi,C.T.,Garry,R.F.,Sabeti,P.C.", "value": "Andersen,K.G.,Shapiro,B.J.,Matranga,C.B.,Gire,S.K.,Sealfon,R.,England,E.M.,Winnicki,S.,Moses,L.M.,Stremlau,M.,Folarin,O.,Odia,I.,Ehiane,P.,Goba,A.,Momoh,M.,Gnirke,A.,Birren,B.,Hensley,L.,Levin,J.Z.,Happi,C.T.,Garry,R.F.,Sabeti,P.C."}, "host": {"value": "Homo sapiens"}, "abbr_authors": {"value": "Andersen et al."}, "clade_membership": {"value": "LIV_V", "confidence": {"LIV_V": 1.0}, "entropy": -1e-12}, "country": {"value": "Sierra Leone"}, "genbank_accession": {"value": "KM821865"}}, "branch_attrs": {"mutations": {"nuc": ["A30G", "C94T", "C129T", "T336C", "C381T", "A533C", "C534T", "T537C", "T549C", "T639C", "C717T", "C726T", "C735T", "T759C", "A855G", "G861A", "C943T", "C957T", "G978A", "G982A", "A1151G", "T1209C", "C1227T", "G1254A", "G1305C", "T1317C", "A1353G", "T1405C", "C1411T", "T1440C"], "GPC": ["N178T", "A328T", "K384R", "H471Y"]}, "labels": {"aa": "GPC: N178T, A328T, K384R, H471Y"}}}, {"name": "M.natalensis-wt/SLE/2019/Largo-00292", "node_attrs": {"div": 0.317, "num_date": {"value": 2019.821, "confidence": [2019.821, 2019.821], "inferred": false}, "accession": "OM735970", "author": {"author": "Ghersi,B.,Vucak,M.,Nichols,J.,Bangura,J.,Davison,A.J.,Bird,B.", "value": "Ghersi,B.,Vucak,M.,Nichols,J.,Bangura,J.,Davison,A.J.,Bird,B."}, "host": {"value": "Mastomys natalensis"}, "division": {"value": "Largo"}, "abbr_authors": {"value": "Ghersi et al."}, "clade_membership": {"value": "LIV_V", "confidence": {"LIV_V": 1.0}, "entropy": -1e-12}, "country": {"value": "Sierra Leone"}, "genbank_accession": {"value": "OM735970"}}, "branch_attrs": {"mutations": {"nuc": ["G33A", "C103T", "C141T", "C147T", "C258T", "T273C", "T339A", "T342C", "T345C", "T396C", "C438T", "G623A", "T672C", "C717A", "T723C", "C786T", "C876T", "T954C", "A960G", "T1062C", "C1101T", "A1215G", "T1413C"], "GPC": ["G208D"]}, "labels": {"aa": "GPC: G208D"}}}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}, "root_sequence": {"nuc": "ATGGGACAAATAGTGACATTCTTCCAGGAAGTGCCTCATGTAATAGAAGAGGTGATGAACATTGTTCTCATTGCACTGTCTGTACTAGCAGTGCTGAAAGGTCTGTACAATTTTGCAACGTGTGGCCTTGTTGGTTTGGTCACTTTCCTCCTGTTGTGTGGTAGGTCTTGCACAACCAGTCTTTATAAAGGGGTTTATGAGCTTCAGACTCTGGAACTAAACATGGAGACACTCAATATGACCATGCCTCTCTCCTGCACAAAGAACAACAGTCATCATTATATAATGGTGGGCAATGAGACAGGACTAGAACTGACCTTGACCAACACGAGCATTATTAATCACAAATTTTGCAATCTGTCTGATGCCCACAAAAAGAACCTCTATGACCACGCTCTTATGAGCATAATCTCAACTTTCCACTTGTCCATCCCCAACTTCAATCAGTATGAGGCAATGAGCTGCGATTTTAATGGGGGAAAGATTAGTGTGCAGTACAACCTGAGTCACAGCTATGCTGGGGATGCAGCCAACCATTGTGGTACTGTTGCAAATGGTGTGTTACAGACTTTTATGAGGATGGCTTGGGGTGGGAGCTACATTGCTCTTGACTCAGGCCGTGGCAACTGGGACTGTATTATGACTAGTTATCAATATCTGATAATCCAAAATACAACCTGGGAAGATCACTGCCAATTCTCGAGACCATCTCCCATCGGTTATCTCGGGCTCCTCTCACAAAGGACTAGAGATATTTATATTAGTAGAAGATTGCTAGGCACATTCACATGGACACTGTCAGATTCTGAAGGTAAAGACACACCAGGGGGATATTGTCTGACCAGGTGGATGCTAATTGAGGCTGAACTAAAATGCTTCGGGAACACAGCTGTGGCAAAATGTAATGAGAAGCATGATGAGGAATTTTGTGACATGCTGAGGCTGTTTGACTTCAACAAACAAGCCATTCAAAGGTTGAAAGCTGAAGCACAAATGAGCATTCAGTTGATCAACAAAGCAGTAAATGCTTTGATAAATGACCAACTTATAATGAAGAACCATCTACGGGACATCATGGGAATTCCATACTGTAATTACAGCAAGTATTGGTACCTCAACCACACAACTACTGGGAGAACATCACTGCCCAAATGTTGGCTTGTATCAAATGGTTCATACTTGAACGAGACCCACTTTTCTGATGATATTGAACAACAAGCTGACAATATGATCACTGAGATGTTACAGAAGGAGTATATGGAGAGGCAGGGGAAGACACCATTGGGTCTAGTTGACCTCTTTGTGTTCAGTACAAGTTTCTATCTTATTAGCATCTTCCTTCACCTAGTCAAAATACCAACTCATAGGCATATTGTAGGCAAGTCGTGTCCCAAACCTCACAGATTGAATCATATGGGCATTTGTTCCTGTGGACTCTACAAACAGCCTGGTGTGCCTGTGAAATGGAAGAGATGA", "GPC": "MGQIVTFFQEVPHVIEEVMNIVLIALSVLAVLKGLYNFATCGLVGLVTFLLLCGRSCTTSLYKGVYELQTLELNMETLNMTMPLSCTKNNSHHYIMVGNETGLELTLTNTSIINHKFCNLSDAHKKNLYDHALMSIISTFHLSIPNFNQYEAMSCDFNGGKISVQYNLSHSYAGDAANHCGTVANGVLQTFMRMAWGGSYIALDSGRGNWDCIMTSYQYLIIQNTTWEDHCQFSRPSPIGYLGLLSQRTRDIYISRRLLGTFTWTLSDSEGKDTPGGYCLTRWMLIEAELKCFGNTAVAKCNEKHDEEFCDMLRLFDFNKQAIQRLKAEAQMSIQLINKAVNALINDQLIMKNHLRDIMGIPYCNYSKYWYLNHTTTGRTSLPKCWLVSNGSYLNETHFSDDIEQQADNMITEMLQKEYMERQGKTPLGLVDLFVFSTSFYLISIFLHLVKIPTHRHIVGKSCPKPHRLNHMGICSCGLYKQPGVPVKWKR*"}} \ No newline at end of file From 91bff2e4f49da4922f832336852649d48dbe3b31 Mon Sep 17 00:00:00 2001 From: Jennifer Chang Date: Thu, 27 Feb 2025 18:56:00 -0800 Subject: [PATCH 4/7] Group reference files in segment folders --- .../lassa_gpc.fasta => phylogenetic/defaults/gpc/reference.fasta | 0 phylogenetic/defaults/{lassa_gpc.gb => gpc/reference.gb} | 0 shared/lassa_l.fasta => phylogenetic/defaults/l/reference.fasta | 0 phylogenetic/defaults/{lassa_l.gb => l/reference.gb} | 0 shared/lassa_s.fasta => phylogenetic/defaults/s/reference.fasta | 0 phylogenetic/defaults/{lassa_s.gb => s/reference.gb} | 0 6 files changed, 0 insertions(+), 0 deletions(-) rename shared/lassa_gpc.fasta => phylogenetic/defaults/gpc/reference.fasta (100%) rename phylogenetic/defaults/{lassa_gpc.gb => gpc/reference.gb} (100%) rename shared/lassa_l.fasta => phylogenetic/defaults/l/reference.fasta (100%) rename phylogenetic/defaults/{lassa_l.gb => l/reference.gb} (100%) rename shared/lassa_s.fasta => phylogenetic/defaults/s/reference.fasta (100%) rename phylogenetic/defaults/{lassa_s.gb => s/reference.gb} (100%) diff --git a/shared/lassa_gpc.fasta b/phylogenetic/defaults/gpc/reference.fasta similarity index 100% rename from shared/lassa_gpc.fasta rename to phylogenetic/defaults/gpc/reference.fasta diff --git a/phylogenetic/defaults/lassa_gpc.gb b/phylogenetic/defaults/gpc/reference.gb similarity index 100% rename from phylogenetic/defaults/lassa_gpc.gb rename to phylogenetic/defaults/gpc/reference.gb diff --git a/shared/lassa_l.fasta b/phylogenetic/defaults/l/reference.fasta similarity index 100% rename from shared/lassa_l.fasta rename to phylogenetic/defaults/l/reference.fasta diff --git a/phylogenetic/defaults/lassa_l.gb b/phylogenetic/defaults/l/reference.gb similarity index 100% rename from phylogenetic/defaults/lassa_l.gb rename to phylogenetic/defaults/l/reference.gb diff --git a/shared/lassa_s.fasta b/phylogenetic/defaults/s/reference.fasta similarity index 100% rename from shared/lassa_s.fasta rename to phylogenetic/defaults/s/reference.fasta diff --git a/phylogenetic/defaults/lassa_s.gb b/phylogenetic/defaults/s/reference.gb similarity index 100% rename from phylogenetic/defaults/lassa_s.gb rename to phylogenetic/defaults/s/reference.gb From 3be0145a552becdcda065fb705fbe61e81ae18c0 Mon Sep 17 00:00:00 2001 From: Jennifer Chang Date: Thu, 27 Feb 2025 18:59:00 -0800 Subject: [PATCH 5/7] Update pipelines with segment reference paths --- ingest/defaults/config.yaml | 2 +- nextclade/rules/annotate_phylogeny.smk | 2 +- phylogenetic/rules/annotate_phylogeny.smk | 2 +- phylogenetic/rules/prepare_sequences.smk | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/ingest/defaults/config.yaml b/ingest/defaults/config.yaml index 9900bb3..34dbb98 100644 --- a/ingest/defaults/config.yaml +++ b/ingest/defaults/config.yaml @@ -117,7 +117,7 @@ curate: ] nextclade: - segment_reference: "../shared/lassa_{segment}.fasta" + segment_reference: "../phylogenetic/defaults/{segment}/reference.fasta" min_seed_cover: 0.01 dataset: "../nextclade_data" field_map: diff --git a/nextclade/rules/annotate_phylogeny.smk b/nextclade/rules/annotate_phylogeny.smk index fbe92e5..6c11101 100644 --- a/nextclade/rules/annotate_phylogeny.smk +++ b/nextclade/rules/annotate_phylogeny.smk @@ -54,7 +54,7 @@ rule translate: input: tree = "results/tree.nwk", node_data = "results/nt_muts.json", - reference = "../phylogenetic/defaults/lassa_gpc.gb" + reference = "../phylogenetic/defaults/gpc/reference.gb" output: node_data = "results/aa_muts.json" log: diff --git a/phylogenetic/rules/annotate_phylogeny.smk b/phylogenetic/rules/annotate_phylogeny.smk index 12c2a9a..f3ef8d1 100644 --- a/phylogenetic/rules/annotate_phylogeny.smk +++ b/phylogenetic/rules/annotate_phylogeny.smk @@ -59,7 +59,7 @@ rule translate: input: tree = "results/{segment}/tree.nwk", node_data = "results/{segment}/nt_muts.json", - reference = "defaults/lassa_{segment}.gb" + reference = "defaults/{segment}/reference.gb" output: node_data = "results/{segment}/aa_muts.json" log: diff --git a/phylogenetic/rules/prepare_sequences.smk b/phylogenetic/rules/prepare_sequences.smk index 6202976..0f5563a 100644 --- a/phylogenetic/rules/prepare_sequences.smk +++ b/phylogenetic/rules/prepare_sequences.smk @@ -128,7 +128,7 @@ rule align: """ input: sequences = "results/{segment}/filtered.fasta", - reference = "defaults/lassa_{segment}.gb" + reference = "defaults/{segment}/reference_.gb" output: alignment = "results/{segment}/aligned.fasta" log: From 3153b6b99e1fe37d6cefb74b573d2d99c0be04f1 Mon Sep 17 00:00:00 2001 From: Jennifer Chang Date: Thu, 27 Feb 2025 19:15:54 -0800 Subject: [PATCH 6/7] fixup --- phylogenetic/rules/prepare_sequences.smk | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/phylogenetic/rules/prepare_sequences.smk b/phylogenetic/rules/prepare_sequences.smk index 0f5563a..ab781e3 100644 --- a/phylogenetic/rules/prepare_sequences.smk +++ b/phylogenetic/rules/prepare_sequences.smk @@ -128,7 +128,7 @@ rule align: """ input: sequences = "results/{segment}/filtered.fasta", - reference = "defaults/{segment}/reference_.gb" + reference = "defaults/{segment}/reference.gb" output: alignment = "results/{segment}/aligned.fasta" log: From 9643d5ba811c8b84c520e6a841fc8a3f66a470bb Mon Sep 17 00:00:00 2001 From: Jennifer Chang Date: Thu, 27 Feb 2025 19:47:47 -0800 Subject: [PATCH 7/7] Update dataset --- nextclade_data/tree.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextclade_data/tree.json b/nextclade_data/tree.json index 2be1a70..1f852f2 100644 --- a/nextclade_data/tree.json +++ b/nextclade_data/tree.json @@ -1 +1 @@ -{"version": "v2", "meta": {"title": "Real-time tracking of Lassa virus evolution", "updated": "2025-02-27", "build_url": "https://github.com/nextstrain/lassa", "data_provenance": [{"name": "GenBank", "url": "https://www.ncbi.nlm.nih.gov/genbank/"}], "maintainers": [{"name": "Jennifer Chang", "url": "https://bedford.io/team/jennifer-chang/"}, {"name": "Richard Daodu", "url": "https://github.com/JoiRichi"}, {"name": "Denise K\u00fchnert", "url": "https://www.shh.mpg.de/person/54587/935000"}, {"name": "the Nextstrain team", "url": "https://nextstrain.org/team"}], "display_defaults": {"map_triplicate": false, "color_by": "clade_membership", "distance_measure": "div"}, "genome_annotations": {"nuc": {"end": 1476, "start": 1, "strand": "+", "type": "source", "seqid": "../phylogenetic/defaults/lassa_gpc.gb"}, "GPC": {"end": 1476, "seqid": "../phylogenetic/defaults/lassa_gpc.gb", "start": 1, "strand": "+", "type": "CDS"}}, "description": "We gratefully acknowledge the authors, originating and submitting laboratories of the genetic sequences and metadata for sharing their work.\n\nSpecial thanks to Richard Daodu and Laura McMullan for comments, code and suggestions.\n\nPlease note that although data generators have generously shared data in an open fashion, that does not mean there should be free license to publish on this data. Data generators should be cited where possible and collaborations should be sought in some circumstances. Please try to avoid scooping someone else's work. Reach out if uncertain.\n\nMuch of the genomic data here comes from publications [Andersen et al 2015](https://doi.org/10.1016/j.cell.2015.07.020), [Siddle et al 2018](https://doi.org/10.1056/NEJMoa1804498\n) and [Kafetzopoulou et al 2019](https://doi.org/10.1126/science.aau9343), but with more recent sequences from NCBI may not yet be published.\n\nWe maintain two views of Lassa virus evolution: one showing evolution of the [L segment](https://nextstrain.org/lassa/l) and the other showing evolution of the [S segment](https://nextstrain.org/lassa/s). A tangle tree showing [co-evolution of L and S](https://nextstrain.org/lassa/l:lassa/s) is also available.\n\n#### Underlying data\n\nWe curate sequence data and metadata from NCBI as the starting point for our analyses. Curated sequences and metadata are available as flat files at:\n\n##### L segment\n* [data.nextstrain.org/files/workflows/lassa/l/sequences.fasta.zst](https://data.nextstrain.org/files/workflows/lassa/l/sequences.fasta.zst)\n* [data.nextstrain.org/files/workflows/lassa/l/metadata.tsv.zst](https://data.nextstrain.org/files/workflows/lassa/l/metadata.tsv.zst)\n\n##### S segment\n* [data.nextstrain.org/files/workflows/lassa/s/sequences.fasta.zst](https://data.nextstrain.org/files/workflows/lassa/s/sequences.fasta.zst)\n* [data.nextstrain.org/files/workflows/lassa/s/metadata.tsv.zst](https://data.nextstrain.org/files/workflows/lassa/s/metadata.tsv.zst)\n\n##### Both segments combined\n* [data.nextstrain.org/files/workflows/lassa/all/sequences.fasta.zst](https://data.nextstrain.org/files/workflows/lassa/all/sequences.fasta.zst)\n* [data.nextstrain.org/files/workflows/lassa/all/metadata.tsv.zst](https://data.nextstrain.org/files/workflows/lassa/all/metadata.tsv.zst)\n\n---\n\nScreenshots may be used under a [CC-BY-4.0 license](https://creativecommons.org/licenses/by/4.0/) and attribution to nextstrain.org must be provided.\n", "colorings": [{"key": "gt", "title": "Genotype", "type": "categorical"}, {"key": "num_date", "title": "Date", "type": "continuous"}, {"key": "country", "title": "Country", "type": "categorical", "scale": [["Sierra Leone", "#4068CF"], ["Guinea", "#5098B9"], ["Liberia", "#6CB28C"], ["C\u00f4te d'Ivoire", "#94BD62"], ["Mali", "#BFBB47"], ["Togo", "#DFA53B"], ["Benin", "#E67131"], ["Nigeria", "#DB2823"]]}, {"key": "division", "title": "Admin Division", "type": "categorical"}, {"key": "host", "title": "Host", "type": "categorical", "scale": [["Homo sapiens", "#4A8CC2"], ["Mastomys", "#71B486"], ["Mastomys erythroleucus", "#ABBD52"], ["Mastomys natalensis", "#DEA73C"]]}, {"key": "abbr_authors", "title": "Authors", "type": "categorical"}, {"key": "clade_membership", "title": "Clade", "type": "categorical"}], "filters": ["country", "division", "host", "abbr_authors", "clade_membership", "lineage_name"], "geo_resolutions": [{"key": "country", "demes": {"Guinea": {"latitude": 10.7226226, "longitude": -10.7083587}, "Liberia": {"latitude": 5.7499721, "longitude": -9.3658524}, "Nigeria": {"latitude": 10.0, "longitude": 8.0}, "C\u00f4te d'Ivoire": {"latitude": 7.9897371, "longitude": -5.5679458}, "Sierra Leone": {"latitude": 8.6400349, "longitude": -11.8400269}, "Benin": {"latitude": 9.961027, "longitude": 2.327362}, "Mali": {"latitude": 16.3700359, "longitude": -2.2900239}, "Togo": {"latitude": 8.88625, "longitude": 1.069709}}}], "panels": ["tree", "map", "entropy"], "extensions": {"clade_node_attrs": [{"name": "lineage_name", "displayName": "Lassa lineage name", "description": "Global lassa lineages based on [citation here]."}], "nextclade": {"pathogen": {"schemaVersion": "3.0.0", "defaultCds": "GPC", "attributes": {"name": "Lassa Global Tree", "reference name": "Josiah", "reference accession": "NC_004296"}, "alignmentParams": {"penaltyGapExtend": 1, "penaltyGapOpen": 8, "penaltyGapOpenInFrame": 9, "penaltyGapOpenOutOfFrame": 10, "penaltyMismatch": 1, "scoreMatch": 5, "retryReverseComplement": true, "allowedMismatches": 10, "minSeedCover": 0.01}, "qc": {"missingData": {"enabled": true, "missingDataThreshold": 20, "scoreBias": 4}, "mixedSites": {"enabled": true, "mixedSitesThreshold": 4}, "frameShifts": {"enabled": true}, "stopCodons": {"enabled": true}, "privateMutations": {"enabled": true, "cutoff": 12, "typical": 4, "weightLabeledSubstitutions": 1, "weightReversionSubstitutions": 1, "weightUnlabeledSubstitutions": 1}, "snpClusters": {"enabled": true, "clusterCutOff": 3, "scoreWeight": 50, "windowSize": 50}}}}}}, "tree": {"name": "NODE_0000000", "node_attrs": {"div": 0, "num_date": {"value": 1634.001, "confidence": [1625.527, 1647.293]}, "clade_membership": {"value": "LII", "confidence": {"LII": 0.372, "LIII": 0.251, "LIV_V": 0.186, "LVII": 0.0981, "LI": 0.0932}, "entropy": 1.477}}, "branch_attrs": 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"Andersen,K.G.,Shapiro,B.J.,Matranga,C.B.,Gire,S.K.,Sealfon,R.,England,E.M.,Winnicki,S.,Moses,L.M.,Stremlau,M.,Folarin,O.,Odia,I.,Ehiane,P.,Goba,A.,Momoh,M.,Gnirke,A.,Birren,B.,Hensley,L.,Levin,J.Z.,Happi,C.T.,Garry,R.F.,Sabeti,P.C.", "value": "Andersen,K.G.,Shapiro,B.J.,Matranga,C.B.,Gire,S.K.,Sealfon,R.,England,E.M.,Winnicki,S.,Moses,L.M.,Stremlau,M.,Folarin,O.,Odia,I.,Ehiane,P.,Goba,A.,Momoh,M.,Gnirke,A.,Birren,B.,Hensley,L.,Levin,J.Z.,Happi,C.T.,Garry,R.F.,Sabeti,P.C."}, "host": {"value": "Homo sapiens"}, "abbr_authors": {"value": "Andersen et al."}, "clade_membership": {"value": "LIV_V", "confidence": {"LIV_V": 1.0}, "entropy": -1e-12}, "country": {"value": "Sierra Leone"}, "genbank_accession": {"value": "KM821796"}}, "branch_attrs": {"mutations": {"nuc": ["C103T", "C270T", "T342C", "G492A", "T507C", "T603C", "C735T", "C868T", "C943T", "G945A", "A987G", "C1089T", "A1394G", "G1461A"], "GPC": ["K465R"]}, "labels": {"aa": "GPC: K465R"}}}, {"name": "G3283-SLE-2013", "node_attrs": 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"Andersen,K.G.,Shapiro,B.J.,Matranga,C.B.,Gire,S.K.,Sealfon,R.,England,E.M.,Winnicki,S.,Moses,L.M.,Stremlau,M.,Folarin,O.,Odia,I.,Ehiane,P.,Goba,A.,Momoh,M.,Gnirke,A.,Birren,B.,Hensley,L.,Levin,J.Z.,Happi,C.T.,Garry,R.F.,Sabeti,P.C.", "value": "Andersen,K.G.,Shapiro,B.J.,Matranga,C.B.,Gire,S.K.,Sealfon,R.,England,E.M.,Winnicki,S.,Moses,L.M.,Stremlau,M.,Folarin,O.,Odia,I.,Ehiane,P.,Goba,A.,Momoh,M.,Gnirke,A.,Birren,B.,Hensley,L.,Levin,J.Z.,Happi,C.T.,Garry,R.F.,Sabeti,P.C."}, "host": {"value": "Homo sapiens"}, "abbr_authors": {"value": "Andersen et al."}, "clade_membership": {"value": "LIV_V", "confidence": {"LIV_V": 1.0}, "entropy": -1e-12}, "country": {"value": "Sierra Leone"}, "genbank_accession": {"value": "KM821865"}}, "branch_attrs": {"mutations": {"nuc": ["A30G", "C94T", "C129T", "T336C", "C381T", "A533C", "C534T", "T537C", "T549C", "T639C", "C717T", "C726T", "C735T", "T759C", "A855G", "G861A", "C943T", "C957T", "G978A", "G982A", "A1151G", "T1209C", "C1227T", "G1254A", "G1305C", "T1317C", "A1353G", "T1405C", "C1411T", "T1440C"], "GPC": ["N178T", "A328T", "K384R", "H471Y"]}, "labels": {"aa": "GPC: N178T, A328T, K384R, H471Y"}}}, {"name": "M.natalensis-wt/SLE/2019/Largo-00292", "node_attrs": {"div": 0.317, "num_date": {"value": 2019.821, "confidence": [2019.821, 2019.821], "inferred": false}, "accession": "OM735970", "author": {"author": "Ghersi,B.,Vucak,M.,Nichols,J.,Bangura,J.,Davison,A.J.,Bird,B.", "value": "Ghersi,B.,Vucak,M.,Nichols,J.,Bangura,J.,Davison,A.J.,Bird,B."}, "host": {"value": "Mastomys natalensis"}, "division": {"value": "Largo"}, "abbr_authors": {"value": "Ghersi et al."}, "clade_membership": {"value": "LIV_V", "confidence": {"LIV_V": 1.0}, "entropy": -1e-12}, "country": {"value": "Sierra Leone"}, "genbank_accession": {"value": "OM735970"}}, "branch_attrs": {"mutations": {"nuc": ["G33A", "C103T", "C141T", "C147T", "C258T", "T273C", "T339A", "T342C", "T345C", "T396C", "C438T", "G623A", "T672C", "C717A", "T723C", "C786T", "C876T", "T954C", "A960G", "T1062C", "C1101T", "A1215G", "T1413C"], "GPC": ["G208D"]}, "labels": {"aa": "GPC: G208D"}}}]}]}]}]}]}]}]}]}]}]}]}]}]}]}]}, "root_sequence": {"nuc": "ATGGGACAAATAGTGACATTCTTCCAGGAAGTGCCTCATGTAATAGAAGAGGTGATGAACATTGTTCTCATTGCACTGTCTGTACTAGCAGTGCTGAAAGGTCTGTACAATTTTGCAACGTGTGGCCTTGTTGGTTTGGTCACTTTCCTCCTGTTGTGTGGTAGGTCTTGCACAACCAGTCTTTATAAAGGGGTTTATGAGCTTCAGACTCTGGAACTAAACATGGAGACACTCAATATGACCATGCCTCTCTCCTGCACAAAGAACAACAGTCATCATTATATAATGGTGGGCAATGAGACAGGACTAGAACTGACCTTGACCAACACGAGCATTATTAATCACAAATTTTGCAATCTGTCTGATGCCCACAAAAAGAACCTCTATGACCACGCTCTTATGAGCATAATCTCAACTTTCCACTTGTCCATCCCCAACTTCAATCAGTATGAGGCAATGAGCTGCGATTTTAATGGGGGAAAGATTAGTGTGCAGTACAACCTGAGTCACAGCTATGCTGGGGATGCAGCCAACCATTGTGGTACTGTTGCAAATGGTGTGTTACAGACTTTTATGAGGATGGCTTGGGGTGGGAGCTACATTGCTCTTGACTCAGGCCGTGGCAACTGGGACTGTATTATGACTAGTTATCAATATCTGATAATCCAAAATACAACCTGGGAAGATCACTGCCAATTCTCGAGACCATCTCCCATCGGTTATCTCGGGCTCCTCTCACAAAGGACTAGAGATATTTATATTAGTAGAAGATTGCTAGGCACATTCACATGGACACTGTCAGATTCTGAAGGTAAAGACACACCAGGGGGATATTGTCTGACCAGGTGGATGCTAATTGAGGCTGAACTAAAATGCTTCGGGAACACAGCTGTGGCAAAATGTAATGAGAAGCATGATGAGGAATTTTGTGACATGCTGAGGCTGTTTGACTTCAACAAACAAGCCATTCAAAGGTTGAAAGCTGAAGCACAAATGAGCATTCAGTTGATCAACAAAGCAGTAAATGCTTTGATAAATGACCAACTTATAATGAAGAACCATCTACGGGACATCATGGGAATTCCATACTGTAATTACAGCAAGTATTGGTACCTCAACCACACAACTACTGGGAGAACATCACTGCCCAAATGTTGGCTTGTATCAAATGGTTCATACTTGAACGAGACCCACTTTTCTGATGATATTGAACAACAAGCTGACAATATGATCACTGAGATGTTACAGAAGGAGTATATGGAGAGGCAGGGGAAGACACCATTGGGTCTAGTTGACCTCTTTGTGTTCAGTACAAGTTTCTATCTTATTAGCATCTTCCTTCACCTAGTCAAAATACCAACTCATAGGCATATTGTAGGCAAGTCGTGTCCCAAACCTCACAGATTGAATCATATGGGCATTTGTTCCTGTGGACTCTACAAACAGCCTGGTGTGCCTGTGAAATGGAAGAGATGA", "GPC": "MGQIVTFFQEVPHVIEEVMNIVLIALSVLAVLKGLYNFATCGLVGLVTFLLLCGRSCTTSLYKGVYELQTLELNMETLNMTMPLSCTKNNSHHYIMVGNETGLELTLTNTSIINHKFCNLSDAHKKNLYDHALMSIISTFHLSIPNFNQYEAMSCDFNGGKISVQYNLSHSYAGDAANHCGTVANGVLQTFMRMAWGGSYIALDSGRGNWDCIMTSYQYLIIQNTTWEDHCQFSRPSPIGYLGLLSQRTRDIYISRRLLGTFTWTLSDSEGKDTPGGYCLTRWMLIEAELKCFGNTAVAKCNEKHDEEFCDMLRLFDFNKQAIQRLKAEAQMSIQLINKAVNALINDQLIMKNHLRDIMGIPYCNYSKYWYLNHTTTGRTSLPKCWLVSNGSYLNETHFSDDIEQQADNMITEMLQKEYMERQGKTPLGLVDLFVFSTSFYLISIFLHLVKIPTHRHIVGKSCPKPHRLNHMGICSCGLYKQPGVPVKWKR*"}} \ No newline at end of file +{"version": "v2", "meta": {"title": "Real-time tracking of Lassa virus evolution", "updated": "2025-02-27", "build_url": "https://github.com/nextstrain/lassa", "data_provenance": [{"name": "GenBank", "url": "https://www.ncbi.nlm.nih.gov/genbank/"}], "maintainers": [{"name": "Jennifer Chang", "url": "https://bedford.io/team/jennifer-chang/"}, {"name": "Richard Daodu", "url": "https://github.com/JoiRichi"}, {"name": "Denise K\u00fchnert", "url": "https://www.shh.mpg.de/person/54587/935000"}, {"name": "the Nextstrain team", "url": "https://nextstrain.org/team"}], "display_defaults": {"map_triplicate": false, "color_by": "clade_membership", "distance_measure": "div"}, "genome_annotations": {"nuc": {"end": 1476, "start": 1, "strand": "+", "type": "source", "seqid": "../phylogenetic/defaults/gpc/reference.gb"}, "GPC": {"end": 1476, "seqid": "../phylogenetic/defaults/gpc/reference.gb", "start": 1, "strand": "+", "type": "CDS"}}, "description": "We gratefully acknowledge the authors, originating and submitting laboratories of the genetic sequences and metadata for sharing their work.\n\nSpecial thanks to Richard Daodu and Laura McMullan for comments, code and suggestions.\n\nPlease note that although data generators have generously shared data in an open fashion, that does not mean there should be free license to publish on this data. Data generators should be cited where possible and collaborations should be sought in some circumstances. Please try to avoid scooping someone else's work. Reach out if uncertain.\n\nMuch of the genomic data here comes from publications [Andersen et al 2015](https://doi.org/10.1016/j.cell.2015.07.020), [Siddle et al 2018](https://doi.org/10.1056/NEJMoa1804498\n) and [Kafetzopoulou et al 2019](https://doi.org/10.1126/science.aau9343), but with more recent sequences from NCBI may not yet be published.\n\nWe maintain two views of Lassa virus evolution: one showing evolution of the [L segment](https://nextstrain.org/lassa/l) and the other showing evolution of the [S segment](https://nextstrain.org/lassa/s). A tangle tree showing [co-evolution of L and S](https://nextstrain.org/lassa/l:lassa/s) is also available.\n\n#### Underlying data\n\nWe curate sequence data and metadata from NCBI as the starting point for our analyses. Curated sequences and metadata are available as flat files at:\n\n##### L segment\n* [data.nextstrain.org/files/workflows/lassa/l/sequences.fasta.zst](https://data.nextstrain.org/files/workflows/lassa/l/sequences.fasta.zst)\n* [data.nextstrain.org/files/workflows/lassa/l/metadata.tsv.zst](https://data.nextstrain.org/files/workflows/lassa/l/metadata.tsv.zst)\n\n##### S segment\n* [data.nextstrain.org/files/workflows/lassa/s/sequences.fasta.zst](https://data.nextstrain.org/files/workflows/lassa/s/sequences.fasta.zst)\n* [data.nextstrain.org/files/workflows/lassa/s/metadata.tsv.zst](https://data.nextstrain.org/files/workflows/lassa/s/metadata.tsv.zst)\n\n##### Both segments combined\n* [data.nextstrain.org/files/workflows/lassa/all/sequences.fasta.zst](https://data.nextstrain.org/files/workflows/lassa/all/sequences.fasta.zst)\n* [data.nextstrain.org/files/workflows/lassa/all/metadata.tsv.zst](https://data.nextstrain.org/files/workflows/lassa/all/metadata.tsv.zst)\n\n---\n\nScreenshots may be used under a [CC-BY-4.0 license](https://creativecommons.org/licenses/by/4.0/) and attribution to nextstrain.org must be provided.\n", "colorings": [{"key": "gt", "title": "Genotype", "type": "categorical"}, {"key": "num_date", "title": "Date", "type": "continuous"}, {"key": "country", "title": "Country", "type": "categorical", "scale": [["Sierra Leone", "#4068CF"], ["Guinea", "#5098B9"], ["Liberia", "#6CB28C"], ["C\u00f4te d'Ivoire", "#94BD62"], ["Mali", "#BFBB47"], ["Togo", "#DFA53B"], ["Benin", "#E67131"], ["Nigeria", "#DB2823"]]}, {"key": "division", "title": "Admin Division", "type": "categorical"}, {"key": "host", "title": "Host", "type": "categorical", "scale": [["Homo sapiens", "#4A8CC2"], ["Mastomys", "#71B486"], ["Mastomys erythroleucus", "#ABBD52"], ["Mastomys natalensis", "#DEA73C"]]}, {"key": "abbr_authors", "title": "Authors", "type": "categorical"}, {"key": "clade_membership", "title": "Clade", "type": "categorical"}], "filters": ["country", "division", "host", 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"ATGGGACAAATAGTGACATTCTTCCAGGAAGTGCCTCATGTAATAGAAGAGGTGATGAACATTGTTCTCATTGCACTGTCTGTACTAGCAGTGCTGAAAGGTCTGTACAATTTTGCAACGTGTGGCCTTGTTGGTTTGGTCACTTTCCTCCTGTTGTGTGGTAGGTCTTGCACAACCAGTCTTTATAAAGGGGTTTATGAGCTTCAGACTCTGGAACTAAACATGGAGACACTCAATATGACCATGCCTCTCTCCTGCACAAAGAACAACAGTCATCATTATATAATGGTGGGCAATGAGACAGGACTAGAACTGACCTTGACCAACACGAGCATTATTAATCACAAATTTTGCAATCTGTCTGATGCCCACAAAAAGAACCTCTATGACCACGCTCTTATGAGCATAATCTCAACTTTCCACTTGTCCATCCCCAACTTCAATCAGTATGAGGCAATGAGCTGCGATTTTAATGGGGGAAAGATTAGTGTGCAGTACAACCTGAGTCACAGCTATGCTGGGGATGCAGCCAACCATTGTGGTACTGTTGCAAATGGTGTGTTACAGACTTTTATGAGGATGGCTTGGGGTGGGAGCTACATTGCTCTTGACTCAGGCCGTGGCAACTGGGACTGTATTATGACTAGTTATCAATATCTGATAATCCAAAATACAACCTGGGAAGATCACTGCCAATTCTCGAGACCATCTCCCATCGGTTATCTCGGGCTCCTCTCACAAAGGACTAGAGATATTTATATTAGTAGAAGATTGCTAGGCACATTCACATGGACACTGTCAGATTCTGAAGGTAAAGACACACCAGGGGGATATTGTCTGACCAGGTGGATGCTAATTGAGGCTGAACTAAAATGCTTCGGGAACACAGCTGTGGCAAAATGTAATGAGAAGCATGATGAGGAATTTTGTGACATGCTGAGGCTGTTTGACTTCAACAAACAAGCCATTCAAAGGTTGAAAGCTGAAGCACAAATGAGCATTCAGTTGATCAACAAAGCAGTAAATGCTTTGATAAATGACCAACTTATAATGAAGAACCATCTACGGGACATCATGGGAATTCCATACTGTAATTACAGCAAGTATTGGTACCTCAACCACACAACTACTGGGAGAACATCACTGCCCAAATGTTGGCTTGTATCAAATGGTTCATACTTGAACGAGACCCACTTTTCTGATGATATTGAACAACAAGCTGACAATATGATCACTGAGATGTTACAGAAGGAGTATATGGAGAGGCAGGGGAAGACACCATTGGGTCTAGTTGACCTCTTTGTGTTCAGTACAAGTTTCTATCTTATTAGCATCTTCCTTCACCTAGTCAAAATACCAACTCATAGGCATATTGTAGGCAAGTCGTGTCCCAAACCTCACAGATTGAATCATATGGGCATTTGTTCCTGTGGACTCTACAAACAGCCTGGTGTGCCTGTGAAATGGAAGAGATGA", 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