Name		Name	Last commit message	Last commit date
Analysis/20190809-overall		Analysis/20190809-overall
Bowtie2_Binary		Bowtie2_Binary
Bowtie2_linux		Bowtie2_linux
Glimmer/bin		Glimmer/bin
Graph and Slides		Graph and Slides
Samtools_1.9		Samtools_1.9
Sickle_Master		Sickle_Master
SimpleMake		SimpleMake
docs		docs
lib		lib
obj		obj
sample-run		sample-run
scripts		scripts
Figure1B_Zeevi_Paper_Test_By_Sur.R		Figure1B_Zeevi_Paper_Test_By_Sur.R
Figure1B_Zeevi_Paper_With_Discrete_Genome.R		Figure1B_Zeevi_Paper_With_Discrete_Genome.R
Find_Replication_Origin.R		Find_Replication_Origin.R
Loess_Regression.R		Loess_Regression.R
Manhattan_Plot_for_Genome_Mapping.R		Manhattan_Plot_for_Genome_Mapping.R
PTR_Boxplot.R		PTR_Boxplot.R
PTR_Cal_Multiple_Input.nf		PTR_Cal_Multiple_Input.nf
PTR_Calculation_Graph.R		PTR_Calculation_Graph.R
PTR_Calculation_Graph_Multiple_Input.R		PTR_Calculation_Graph_Multiple_Input.R
PTR_Calculation_Single_and_Paired.nf		PTR_Calculation_Single_and_Paired.nf
README.md		README.md
Working_With_Sam_Files.R		Working_With_Sam_Files.R
nextflow		nextflow

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Microbiota-Project

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Calculate Peak-to-Trough Ratio (PTR), plot coverage graph, and perform quality control over contigs in a single pipeline integrating Glimmer3, Bowtie2, Sickle, and algorithms in R.

bam genome-alignment genome-graph genome-preprocessing genomics microbiota pipeline r sam sequence

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