Three tables generated as part of MBO WP2's work on identifying primers, reference databases and pipelines used for metabarcoding studies. The first table serves as an excellent starting point for ctrl+F searches for given primer sequences, e.g. when comparing across studies. We specifically include both 5'-3' and 3'-5' primer sequences to enable this ctrl+F search, as the same primers are sometimes reported in diferrent directions across studies. The second table identifies key reference databases often encountered in the literature, with specific details associated with each of them. The third table is a comprehensive (but likely incomplete) list of pipelines for processing metabarcoding data, providing external links to where to find more information about each of them.
Table 1: An incomplete overview of empirically tested and/or frequently used metabarcoding primers and their target groups. For more exhaustive lists of metabarcoding primers found in the literature, see Pieter Proovost's list of eDNA metabarcoding primers and the paper by Takahashi et al. 2023.
| Primer combination name | Individual primer names (F and R) | F-primer (5′-3′) F-primer (3′-5′) |
R-primer (5′-3′) R-primer (3′-5′) |
Marker gene | Target group | Fragment size (bp) | Reference(s) | Additional usage notes and other relevant information |
|---|---|---|---|---|---|---|---|---|
18S_allshorts |
F: 18S_allshorts forward R: 18S_allshorts reverse |
TTTGTCTGSTTAATTSCG GCSTTAATTSGTCTGTTT |
TCACAGACCTGTTATTGC CGTTATTGTCCAGACACT |
18S (V7) | Eukaryotes | ~110 | Guardiola et al. (2015) | Highly specific for eukaryotes. Amplifies same region as Hardy et al. (2010), with almost same resolution for 40 bp less. |
18S_allshorts (mod. "Euka02") |
F: 18S_allshorts forward R: 18S_allshorts reverse (mod.) |
TTTGTCTGSTTAATTSCG GCSTTAATTSGTCTGTTT |
CACAGACCTGTTATTGC CGTTATTGTCCAGACAC |
18S (V7) | Eukaryotes | ~110 | Guardiola et al. (2015), Taberlet et al. (2018) | First "T" omitted compared to original reverse primer to better equilibrate the melting temperatures of the two primers. |
Aves01 |
F: Aves_12Sa R: Aves_12Sc |
GATTAGATACCCCACTATGC CGTATCACCCCATAGATTAG |
GTTTTAAGCGTTTGTGCTCG GCTCGTGTTTGCGAATTTTG |
12S | Aves (birds) | ~52 | Epp et al. (2012) | Limited taxonomic resolution, but highly specific to birds. |
Arch01 |
F: Arch01-F R: Arch01-R |
CCTGCTCCTTGCACACAC CACACACGTTCCTCGTCC |
CCTACGGCTACCTTGTTAC CATTGTTCCATCGGCATCC |
16S (V9) | Archaea | ~85 | Taberlet et al. (2018) | Highly specific of Archaea. |
Baci01 |
F: Baci01-F R: Baci01-R |
ATTCCAGCTCCAATAGCGTA ATGCGATAACCTCGACCTTA |
CTTTRAACRCLCTRATTTYTTCAC CACTTYTTTARTCLCRCAARTTTC |
18S (V4) | Bacillariophyta (diatoms) | ~150 | Taberlet et al. (2018) | Will also amplify other eukaryotes. |
Bact02 |
F: Bact02-F R: Bact02-R |
GCCAGCMGCCGCGGTAA AATGGCGCCGMCGACCG |
GGACTACCMGGGTATCTAA AATCTATGGGMCCATCAGG |
16S (V4) | Bacteria+Archaea | ~254 | Taberlet et al. (2018) | |
Bact03 |
F: Bact03-F R: 806RB |
GTGYCAGCMGCCGCGGTAA AATGGCGCCGMCGACYGTG |
GGACTACNVGGGTWTCTAAT TAATCTWTGGGVNCATCAGG |
16S (V4) | Bacteria+Archaea | ~253 | Baker et al. (2003), Quince et al. (2011), Apprill et al. (2015) | Recommended by Earth Microbiome Project. Not necessary to degenerate both primers if only targeting bacteria (Taberlet et al. 2018). There appears to be a couple of different versions of the F-primer, with "GTGCCAGCMGCCGCGGTAA" reported by Baker et al. (2003), "GTGNCAGCMGCCGCGGTAA" reported by Quince et al. (2011), and "GTGYCAGCMGCCGCGGTAA" first reported by Watanabe et al. (2001) and later Asami et al. (2005) |
Bact04 |
F: Bact03-F R: R926 |
GTGYCAGCMGCCGCGGTAA AATGGCGCCGMCGACYGTG |
CCGYCAATTYMTTTRAGTTT TTTGARTTTMYTTAACYGCC |
16S (V4-V5) | Bacteria+Archaea | ~373-378 | Baker et al. (2003), Quince et al. (2011) | Recommended by Earth Microbiome Project. Also amplifies a relatively large number of eukaryotes (Taberlet et al. 2018). |
BACTB |
F: BACTB-F R: BACTB-R |
GGATTAGATACCCTGGTAGT TGATGGTCCCATAGATTAGG |
CACGACACGAGCTGACG GCAGTCGAGCACAGCAC |
16S (V5-V6) | Bacteria | ~258 | Fliegerova et al. (2014) | |
Balzano |
F: TAReuk454FWD1 (V4F) R: V4RB |
CCAGCASCYGCGGTAATTCC CCTTAATGGCGYCSACGACC |
ACTTTCGTTCTTGATYRR RRYTAGTTCTTGCTTTCA |
18S (V4) | Eukaryotes | ~380 | Stoeck et al. (2010), Balzano et al. (2015) | |
Banos |
F: nu-SSU-1333-5′ (FF390) R: nu-SSU-1647-3′ (FR-1) |
CGATAACGAACGAGACCT TCCAGAGCAAGCAATAGC |
AICCATTCAATCGGTAIT TIATGGCTAACTTACCIA |
18S (V7-V8) | Fungi | ~348 | Banos et al. (2018) | Note that “I” (inosine) often gets replaced with “N” for bioinformatic software to recognize the wobble-base. |
Batr01 |
F: batra_F R: batra_R |
ACACCGCCCGTCACCCT TCCCACTGCCCGCCACA |
GTAYACTTACCATGTTACGACTT TTCAGCATTGTACCATTCAYATG |
12S | Batrachia (frogs and salamanders) | ~51 | Valentini et al. (2016) | |
Berry 16S-Fish |
F: Fish16sF/D R: 16s2R (degenerate) |
GACCCTATGGAGCTTTAGAC CAGATTTCGAGGTATCCCAG |
CGCTGTTATCCCTADRGTAACT TCAATGRDATCCCTATTGTCGC |
16S | Fishes | ~200 | Berry et al. (2017), Deagle et al. (2007) | |
BF1/BR1 |
F: BF1 R: BR1 |
ACWGGWTGRACWGTNTAYCC CCYATNTGWCARGTWGGWCA |
ARYATDGTRATDGCHCCDGC CGDCCHCGDTARTGDTAYRA |
COI | Macroinvertebrates | 217 | Elbrecht & Leese (2017) | Designed for mock communities, so co-amplifies a lot of undesired taxa when applied to eDNA samples. |
Bryo01 |
F: bryo_P6F R: Bryo01-R |
GATTCAGGGAAACTTAGGTTG GTTGGATTCAAAGGGACTTAG |
CCATYGAGTCTCTGCACC CCACGTCTCTGAGYTACC |
trnL | Bryophyta | ~53 | Epp et al. (2012), Taberlet et al. (2018) | One degenerated bp in reverse primer compared to Epp et al. (2012). |
Caporaso |
F: F515 R: R806 |
GTGCCAGCMGCCGCGGTAA AATGGCGCCGMCGACCGTG |
GGACTACHVGGGTWTCTAAT TAATCTWTGGGVHCATCAGG |
16S | Bacteria | ~253 | Baker et al. (2003), Caporaso et al. (2011) | |
Cole01 |
F: Cole01-F R: Cole01-R |
TGCWAAGGTAGCATAATMATTAG GATTAMTAATACGATGGAAWCGT |
TCTATAGGGTCTTCTCGTC CTGCTCTTCTGGGATATCT |
16S | Coleoptera (beetles) | ~107 | Taberlet et al. (2018) | Modified primers from Epp et al. (2012). Also amplifies other metazoans. |
Coll01 |
F: COLA R: COLB |
ACGCTGTTATCCCTWAGG GGAWTCCCTATTGTCGCA |
GACGATAAGACCCTWTAGA AGATWTCCCAGAATAGCAG |
16S | Collembola (springtails) | ~132 | Janssen et al. (2017) | |
Culi01 |
F: Culicidae-f R: Culicidae-r |
ACGCTGTTATCCCTAAGGTAACTTA ATTCAATGGAATCCCTATTGTCGCA |
GACGAGAAGACCCTATAGATCTTTAT TATTTCTAGATATCCCAGAAGAGCAG |
16S | Culicidae (mosquitos) | ~145 | Schneider et al. (2016) | |
Cyan01 |
F: Cyan01-F R: Cyan01-R |
CTYAAGCCGACATTCTCAC CACTCTTACAGCCGAAYTC |
GACAACYAGGAGGTTTGC CGTTTGGAGGAYCAACAG |
23S | Cyanobacteria | ~180 | Taberlet et al. (2018) | |
Elas02 |
F: Elas02-F R: Elas02-R |
GTTGGTHAATCTCGTGCCAGC CGACCGTGCTCTAAHTGGTTG |
CATAGTAGGGTATCTAATCCTAGTTTG GTTTGATCCTAATCTATGGGATGATAC |
12S | Elasmobranchii | ~182 | Taberlet et al. (2018) | |
Ench01 |
F: Ench_12Sa R: Ench_12Sc |
GCTGCACTTTGACTTGAC CAGTTCAGTTTCACGTCG |
AGCCTGTGTACTGCTGTC CTGTCGTCATGTGTCCGA |
12S | Enchytraeidae | ~48 | Epp et al. (2012) | |
Euka01 |
F: All18SF R: All18SR |
TGGTGCATGGCCGTTCTTAGT TGATTCTTGCCGGTACGTGGT |
CATCTAAGGGCATCACAGACC CCAGACACTACGGGAATCTAC |
18S (V7) | Eukaryotes | ~161 | Hardy et al. (2010) | Highly specific of eukaryotes. Much longer fragment for certain insects, amphipods and isopods (Taberlet et al. 2018). |
Euka03 |
F: Euka03-F R: Euka03-R |
CCCTTTGTACACACCGCC CCGCCACACATGTTTCCC |
CTTCYGCAGGTTCACCTAC CATCCACTTGGACGYCTTC |
18S (V9) | Eukaryotes | ~133 | Taberlet et al. (2018) | 18S V9 has less reference sequences than V7, but this marker should provide higher taxonomic resolution and has a more standardized fragment size (Taberlet et al. 2018). |
Euk1391f-EukBr |
F: Euk1391f R: EukBr |
GTACACACCGCCCGTC CTGCCCGCCACACATG |
TGATCCTTCTGCAGGTTCACCTAC CATCCACTTGGACGTCTTCCTAGT |
18S (V9) | Eukaryotes | ~128 | Amaral-Zettler et al. (2009), Stoeck et al. (2010), https://earthmicrobiome.org/protocols-and-standards/18s/ | Highly specific of eukaryotes. Used by Earth Microbiome Project. The reverse primer is not optimal. Described as “Euka04” in Taberlet et al. (2018). |
Fung01 |
F: ITS5 R: Fung01-R |
GGAAGTAAAAGTCGTAACAAGG GGAACAATGCTGAAAATGAAGG |
CCAAGAGATCCGTTGYTGAAAGT TGAAAGTYGTTGCCTAGAGAACC |
ITS1 | Fungi | ~226 | Epp et al. (2012) | Does not properly amplify Glomeromycota. Highly variable fragment length for some fungi (Taberlet et al. 2018). Reverse primer appears inspired from Epp et al. (2012), but is not identical to "5.8S_fungi" (CAAGAGATCCGTTGTTGAAAGTT) |
Fung02 |
F: ITS5 R: Fung02-R |
GGAAGTAAAAGTCGTAACAAGG GGAACAATGCTGAAAATGAAGG |
CAAGAGATCCGTTGYTGAAAGTK KTGAAAGTYGTTGCCTAGAGAAC |
ITS1 | Fungi | ~225 | Epp et al. (2012), Taberlet et al. (2018) | Modified version of Epp et al (2012)’s reverse primer to properly amplify Glomeromycota. Highly variable fragment length for some fungi (Taberlet et al. 2018). |
Hadziavdic 18S |
F: F-566 R: R-1200 |
CAGCAGCCGCGGTAATTCC CCTTAATGGCGCCGACGAC |
CCCGTGTTGAGTCAAATTAAGC CGAATTAAACTGAGTTGTGCCC |
18S (V4-V5) | Eukaryotes | ~654 | Hadziavdic et al., 2014 | |
Inse01 |
F: Inse01-F R: Inse01-R |
RGACGAGAAGACCCTATARA ARATATCCCAGAAGAGCAGR |
ACGCTGTTATCCCTAARGTA ATGRAATCCCTATTGTCGCA |
16S | Insecta | ~155 | Taberlet et al. (2018) | Close to the Clarke et al. (2014) primers. |
Isop01 |
F: Isop01-F R: Isop01-R |
ATTTCAGGTCAAGGTGCAGCTT TTCGACGTGGAACTGGACTTTA |
ATTACAACCAAATCCAATTTCA ACTTTAACCTAAACCAACATTA |
12S | Isoptera (termites) | ~66 | Taberlet et al. (2018) | |
Leray |
F: mlCOIintF R: jgHCO2198 |
GGWACWGGWTGAACWGTWTAYCCYCC CCYCCYATWTGWCAAGTWGGWCAWGG |
TAIACYTCIGGRTGICCRAARAAYCA ACYAARAARCCIGTRGGICTYCAIAT |
COI | Metazoans | 313 | Leray et al. (2013), Geller et al. (2013) | Note that “I” (inosine) often gets replaced with “N” for bioinformatic software to recognize the wobble-base. |
Leray-XT |
F: mlCOIintF-XT R: jgHCO2198 |
GGWACWRGWTGRACWITITAYCCYCC CCYCCYATITIWCARGTWGRWCAWGG |
TAIACYTCIGGRTGICCRAARAAYCA ACYAARAARCCIGTRGGICTYCAIAT |
COI | Metazoans | 313 | Geller et al. (2013), Wangensteen et al. (2018) | |
Lumb01 |
F: Lumb01-F R: Lumb01-R |
CAAGAAGACCCTATAGAGCTT TTCGAGATATCCCAGAAGAAC |
GGTCGCCCCAACCGAAT TAAGCCAACCCCGCTGG |
16S | Lumbricina (earthworms) | ~31 | Bienert et al. (2012) | |
Lumb02 |
F: Lumb02-F R: Lumb02-R |
ATTCGGTTGGGGCGACC CCAGCGGGGTTGGCTTA |
CTGTTATCCCTAAGGTAGCTT TTCGATGGAATCCCTATTGTC |
16S | Lumbricina (earthworms) | ~74 | Bienert et al. (2012) | |
Mamm01 |
F: Mamm01-F R: Mamm01-R |
CCGCCCGTCACCCTCCT TCCTCCCACTGCCCGCC |
GTAYRCTTACCWTGTTACGAC CAGCATTGTWCCATTCRYATG |
12S | Mammals | ~58 | Taberlet et al. (2018) | |
Mamm02 |
F: Mamm02-F R: MamP007R |
CGAGAAGACCCTRTGGAGCT TCGAGGTRTCCCAGAAGAGC |
CCGAGGTCRCCCCAACC CCAACCCCRCTGGAGCC |
16S | Mammals | ~74 | Taberlet et al. (2018), Giguet-Covex et al. (2014) | Forward primer slightly modified from Giguet-Covex et al. (2014). Also amplifies some other vertebrates. |
MarVer1 |
F: MarVer1F R: MarVer1R |
CGTGCCAGCCACCGCG GCGCCACCGACCGTGC |
GGGTATCTAATCCYAGTTTG GTTTGAYCCTAATCTATGGG |
12S | Vertebrates | ~202 | Valsecchi et al. (2020) | |
MarVer2 |
F: MarVer2F R: MarVer2R |
CCGCCCGTCACYCTC CTCYCACTGCCCGCC |
CTTACCWTGTTACGACTT TTCAGCATTGTWCCATTC |
12S | Vertebrates | ~89 | Valsecchi et al. (2020) | |
MarVer3 |
F: MarVer3F R: MarVer3R |
AGACGAGAAGACCCTRTG GTRTCCCAGAAGAGCAGA |
GGATTGCGCTGTTATCCC CCCTATTGTCGCGTTAGG |
16S | Vertebrates | ~245 | Valsecchi et al. (2020) | |
Meta01 |
F: Meta01-F R: Meta01-R |
YYCRMCTGTTTAYCAAAAACA ACAAAAACYATTTGTCMRCYY |
CCGGTYTGAACTCARATC CTARACTCAAGTYTGGCC |
16S | Metazoa | ∼548 | Taberlet et al. (2018) | Close to primers designed by Palumbi et al. (2002). Quite long fragment amplified, not likely to work for degraded samples. |
MiFish-E |
F: MiFish-E-F R: MiFish-E-R |
GTTGGTAAATCTCGTGCCAGC CGACCGTGCTCTAAATGGTTG |
CATAGTGGGGTATCTAATCCTAGTTTG GTTTGATCCTAATCTATGGGGTGATAC |
12S | Fishes/vertebrates | 170–185 | Miya et al. (2015) | Elasmobranch-optimized. |
MiFish-U |
F: MiFish-U-F R: MiFish-U-R |
GTCGGTAAAACTCGTGCCAGC CGACCGTGCTCAAAATGGCTG |
CATAGTGGGGTATCTAATCCCAGTTTG GTTTGACCCTAATCTATGGGGTGATAC |
12S | Fishes/vertebrates | 163–185 | Miya et al. (2015) | Universal version. |
MiFish-U (UiT mod.) |
F: MiFish-U-F (UiT mod.) R: MiFish-U-R |
GCCGGTAAAACTCGTGCCAGC CGACCGTGCTCAAAATGGCCG |
CATAGTGGGGTATCTAATCCCAGTTTG GTTTGACCCTAATCTATGGGGTGATAC |
12S | Fishes/vertebrates | 163–185 | Miya et al. (2015), Sales et al. (2019) | Note that the second base in the F primer has been replaced compared to the original. |
Parada |
F: 1389 F R: 1510 R |
TTGTACACACCGCCC CCCGCCACACATGTT |
CCTTCYGCAGGTTCACCTAC CATCCACTTGGACGCTTCC |
16S(V4-V5)/18S(V4) | Universal | ~180 | Parada et al. (2016) | |
Poly01 |
F: Poly01-F R: Poly01-R |
CCGGTYTGAACTCAGMTCA ACTMGACTCAAGTYTGGCC |
TGGCACCTCGATGTTGGCT TCGGTTGTAGCTCCACGGT |
16S | Polychaetes | ~63 | Taberlet et al. (2018) | |
Riaz1 |
F: F1 R: R1 |
ACTGGGATTAGATACCCC CCCCATAGATTAGGGTCA |
TAGAACAGGCTCCTCTAG GATCTCCTCGGACAAGAT |
12S | Vertebrates | ~106 | Riaz et al. (2011) | |
Riaz2 (12S-V5) |
F: 12S-V5-F R: 12S-V5-R |
TAGAACAGGCTCCTCTAG GATCTCCTCCGACAAAGT |
TTAGATACCCCACTATGC GCATAGTGGGGTATCTAA |
12S | Vertebrates | ~97 | Riaz et al. (2011) | |
Sper01 |
F: g-A49425 (Sper01-F) R: h-B49466 (Sper01-R) |
GGGCAATCCTGAGCCAA AACCGAGTCCTAACGGG |
CCATTGAGTCTCTGCACCTATC CTATCCACGTCTCTGAGTTACC |
trnL, P6 loop | Spermatophyta (seed plants) | ~48 | Taberlet et al. (2007) | Widely used for degraded material due to the short length. |
Stoeck |
F: TAReuk454FWD1 (V4F) R: TAReukREV3 (V4R) |
CCAGCASCYGCGGTAATTCC CCTTAATGGCGYCSACGACC |
ACTTTCGTTCTTGATYRA ARYTAGTTCTTGCTTTCA |
18S (V4) | Eukaryotes | ~380 | Stoeck et al. (2010) | |
Tele01 |
F: teleo_F R: teleo_R |
ACACCGCCCGTCACTCT TCTCACTGCCCGCCACA |
CTTCCGGTACACTTACCATG GTACCATTCACATGGCCTTC |
12S | Teleostei | ~64 | Valentini et al. (2016) | Poor resolution for Cyprinidae and Gadidae. |
Tele02 |
F: Tele02-F R: Tele02-R |
AAACTCGTGCCAGCCACC CCACCGACCGTGCTCAAA |
GGGTATCTAATCCCAGTTTG GTTTGACCCTAATCTATGGG |
12S | Fishes/vertebrates | 129-209 | Taberlet et al. (2018), Thomsen et al. (2016) | F-primer first described as "V05F_898" from Thomsen et al. (2016). |
| Database | Target group | Website/download link | Marker(s) | Known deficiencies | Last updated | Licence type | Coverage (Regions) | Additional usage notes and other relevant information |
|---|---|---|---|---|---|---|---|---|
BOLD |
Animals, plants, fungi | https://boldsystems.org/ | COI, rbcL, matK, ITS, 18S, 12S | Lack of prokaryotes. Taxonomic backbone different to other databases. Needs curation. | Frequent updates | Open/Restricted | Worldwide | Widely used database for species-level identification in DNA barcoding |
DDBJ |
General | https://www.ddbj.nig.ac.jp/services/index-e.html?tag=database | All | Mirrors NCBI and ENA; metadata in Japanese | Continuous | Data is shared freely among DDBJ, NCBI, and ENA | Worldwide | DNA DataBank of Japan — part of the International Nucleotide Sequence Database Collaboration (INSDC). |
eKOI |
Eukaryotes, protists | https://github.com/rubenmiguens/eKOI_taxonomy_database/ | COI | New and relatively untested | Uncertain | Not specified | Worldwide | Curated GenBank and mitogenome sequences, focusing on protists |
ENA (formerly EMBL) |
General | https://www.ebi.ac.uk/ena/browser/home | All | Low curation and heterogeneous metadata across submissions; sequences include both validated and unverified entries. | Continuous | Data is shared freely among DDBJ, NCBI, and ENA | Worldwide | European Nucleotide Archive; part of INSDC. |
ENSEMBL |
Eukaryotic genomes | https://ensembl.org/ | Genomic | Focus on model and medically relevant organisms | Continuous | CC BY 4.0 | Worldwide | Genome browser integrating multiple assemblies and annotations. |
FlyBase |
Insects, Drosophila spp. | https://flybase.org/ | Genomic and transcriptomic | Focused on model Drosophila species; not representative of insect diversity | Continuous | CC BY 4.0 | Worldwide (model species) | Comprehensive curated source for Drosophila genomics; mainly relevant for model-organism studies rather than environmental surveys |
GOLD |
Microbes (genomes, metagenomes) | https://gold.jgi.doe.gov/ | Genomic, metagenomic | Metadata quality depends on submitter; limited marker-level annotation | Continuous | Open | Worldwide | Genomes OnLine Database—metadata registry for microbial genomes and metagenomes; often used to track projects integrated into IMG |
GreenGenes2 |
Bacteria, Archaea | https://ftp.microbio.me/greengenes_release/current/ | 16S rRNA | Superseded by SILVA/GTDB; limited recent updates; partial taxonomy inconsistencies | 2024-09-xx | BSD 2-Clause License, but with a 3rd clause that prohibits others from using the name of the copyright holder or its contributors to promote derived products without written consent. | Worldwide | Outdated but still used in some microbial studies |
GTDB |
Bacteria, Archaea | https://gtdb.ecogenomic.org/ | 16S, genomes | Only prokaryotes; taxonomy differs from NCBI | 2025-04-16 | CC BY 4.0 | Worldwide | Widely used for standardized bacterial and archaeal taxonomy. |
HMP |
Human microbiome | https://microbiomedb.org/mbio/app | 16S, WGS | Limited to human-associated microbiomes; not applicable to environmental or non-human samples; and not updated on a regular basis | 2024-05-07 | CC BY 4.0 | Worldwide | Human Microbiome Project reference set. |
IMG |
Microbes (genomes, metagenomes, metatranscriptomes) | https://img.jgi.doe.gov/ | Whole genomes, 16S, functional genes | Annotation and taxonomy depend on submitter metadata; not optimized for marker-gene metabarcoding workflows | Continuous | DOE Data Policy (open for publicly released datasets) | Worldwide | Integrated Microbial Genomes (IMG) system maintained by JGI; provides analysis tools for genome, metagenome, and metatranscriptome datasets; linked to GOLD for project metadata |
KEGG |
General (functional genes, pathways) | https://www.genome.jp/kegg/ | Functional genes | Primarily pathway-focused; limited taxonomic coverage and sequence-level annotation | Continuous | CC BY-NC 4.0 | Worldwide | Kyoto Encyclopedia of Genes and Genomes; integrates genomic and metabolic information for pathway and functional analyses |
MetaPhlAn |
Microbiomes (taxonomic profiling) | https://huttenhower.sph.harvard.edu/metaphlan/ | Marker genes | Primarily human-associated; not suitable for general environmental communities | 2023-11-10 | CC BY 4.0 | Worldwide | Database of unique clade-specific marker genes used by MetaPhlAn for taxonomic profiling of microbial communities |
MIDORI2 |
Eukaryotes | https://www.reference-midori.info/ | Many markers | No prokaryotes included | Updates occur with every GenBank update | CC BY 4.0 | Worldwide | MIDORI2 comes in two curated versions, either with or without binomial species descriptions, such as "cf.," "aff.," and "sp." |
NCBI nr |
General | https://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/ | Any | Low curation and heterogeneous metadata across submissions; sequences include both validated and unverified entries. | Continuous | Data is shared freely among DDBJ, NCBI, and ENA | Worldwide | Comprehensive non-redundant version of NCBI nt |
NCBI nt |
General | https://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/ | Any | Low curation and heterogeneous metadata across submissions; sequences include both validated and unverified entries. | Continuous | Data is shared freely among DDBJ, NCBI, and ENA | Worldwide | Comprehensive but includes uncurated and redundant sequences |
NCBI RefSeq |
Curated representative taxa | https://ftp.ncbi.nlm.nih.gov/refseq/ | Full genomes and individual gene sequences (including common barcoding markers). | Continuous | Open | Worldwide | Data is shared freely among DDBJ, NCBI, and ENA | Curated, non-redundant subset of INSDC sequences; standardized annotations for reference genomes |
NordicRefDBs |
Nordic Marine eDNA | https://github.com/MadsRJ/NordicRefDBs | COI, 12S | Regional scope; under development | 2025 (beta) | CC BY 4.0 | Nordic Seas | Regionally curated database initiative focusing on species from Nordic countries. |
PDB |
Proteins, macromolecular structures | https://www.rcsb.org/ | Protein structures | Limited nucleotide data; experimental bias toward crystallizable proteins | Continuous | CC0 | Worldwide | Protein Data Bank—key archive for experimentally determined 3D structures; relevant for structural bioinformatics |
Pfam |
Protein families | http://pfam.xfam.org/ | Protein sequences (domains) | Functional, not taxonomic focus; limited marker-level application | 2025-06-19 | CC0 | Worldwide | Curated collection of protein domains and families; used for functional and phylogenetic annotation |
Phytozome |
Plants | https://phytozome-next.jgi.doe.gov/ & https://academic.oup.com/nar/article/40/D1/D1178/2903577?login=true | Genomes | Continuously | Creative Commons Attribution 4.0 International License | Worldwide | Relevant if exploring nuclear plant markers, otherwise not | |
PR2 |
Protists | https://pr2-database.org/ | 18S | 2025-04-02 | MIT License | Worldwide | Specialized and curated for protist ribosomal sequences | |
RDP |
Bacteria, Archaea, Fungi | 16S, 28S | Worldwide | Focused on ribosomal RNA sequences, ideal for microbial metabarcoding. | ||||
Silva |
Microbes, eukaryotes | https://www.arb-silva.de/ | 16S, 18S, 23S, 28S | Taxonomic inconsistencies, biases toward well-studied organisms, sequence quality issues | 2024-07-11 | CC BY 4.0 | Worldwide | A comprehensive online resource for quality checked and aligned ribosomal RNA sequence data |
TARA Oceans |
Marine microbes, plankton | https://www.ocean-microbiome.org/ | 16S, 18S, metagenomic markers genetic and functional profiles | Ocean-focused; uneven coverage across depth zones and taxa | 2019-11-12 | Open | Global ocean | TARA Oceans reference dataset integrates global planktonic metagenomes and marker genes; foundational for marine microbiome and virome studies |
UNITE |
Fungi | https://unite.ut.ee/ | ITS | Limited to fungal taxa | 2025-06-17 | CC0 | Worldwide | Specialized for fungal ITS sequences |
WormBase |
C. elegans and related nematodes | https://www.alliancegenome.org/members/wormbase | Genomic and transcriptomic | Focused on model C. elegans; limited to nematodes | News and discussions on website, updates regularly | CC BY 4.0 | Worldwide (model species) | Comprehensive curated source for nematode genomics; mainly relevant for model-organism studies rather than environmental surveys |
ZFIN |
Danio rerio (zebrafish) | https://zfin.org/ | Genomic | Creative Commons Attribution 4.0 International License | Zebrafish are native to South Asia, but sold worldwide in aquarium trade | Only relevant for studies of the model organism zebrafish |
Table 3: An alphabetically ordered, incomplete overview of existing metabarcoding pipelines. The metadata for the pipelines is based on information available on GitHub repositories, associated publications, and/or other documentation, and recorded by categories defined in the FAIRe project.
| Pipeline | Link | incl_Data_Challenge | Language | relevant_marker | error_rate_tool | ASV_OTU | otu_raw_description | tax_assign_cat | otu_seq_comp_appr | tax_class_collapse |
|---|---|---|---|---|---|---|---|---|---|---|
AMPtk |
https://github.com/nextgenusfs/amptk/ | No | Python/R/Other | Any | UPARSE/DADA2/UNOISE2/UNOISE3 | User defined | Spike-in filtering | Sequence similarity/Sequence composition | Hybrid/modular | LCA |
Anacapa |
https://github.com/limey-bean/Anacapa/ | Yes | Python/Shell/R | Any | DADA2 | ASV | Other | bowtie2-blca | NA | |
APSCALE |
https://github.com/DominikBuchner/apscale/ | Yes | Python | Any | vsearch/DnoisE | ASV/OTU | LULU | Sequence similarity/Sequence composition | BOLDIGGER3/vsearch SINTAX | NA |
Banzai |
https://github.com/jimmyodonnell/banzai/ | No | Shell/R/Python/HTML/Ruby | Any | vsearch/Swarm | OTU | Sequence similarity | blast | NA | |
Barque |
https://github.com/enormandeau/barque/ | No | Python/Shell/R | Any | vsearch/unoise3 | ASV | Sequence similarity/Sequence composition | vsearch/blast | NA | |
BIOCOM-PIPE |
https://doi.org/10.1186/s12859-020-03829-3 & https://forge.inrae.fr/biocom/biocom-pipe | No | Perl/Python/HTML/Java/CSS | 16S, 18S, 23S | Custom | OTU | Sequence composition | rdp/other | LCA/other | |
Cascabel |
https://github.com/AlejandroAb/CASCABEL/ | Yes | Python/Java/R/Shell/Perl | Any | Other/DADA2 | ASV/OTU | Sequence similarity/Sequence composition | vsearch/DADA2 | LCA/NA | |
CoMA3 |
https://github.com/SebH87/CoMA3/ | No | Python/Shell | 16S/18S/23S/28S/ITS | DADA2/Unoise3/vsearch | OTU | Sequence similarity/Sequence composition | rdp/other | LCA | |
DADA2 |
https://benjjneb.github.io/dada2/tutorial.html | Yes | R | Any | DADA2 | ASV | Sequence similarity/Sequence composition | DADA2 | NA | |
Dadaist2 |
https://github.com/quadram-institute-bioscience/dadaist2/ | No | HTML/UnrealScript/Perl/R/Python/Nextflow/Other | Any | DADA2 | ASV | Sequence similarity/Sequence composition | DECIPHER/DADA2 | LCA/other | |
dadasnake |
https://github.com/a-h-b/dadasnake/ | No | Python/R/Shell | 16S/ITS/Any | DADA2 | ASV/OTU | Sequence similarity/Sequence composition | MOTHUR/DECIPHER | LCA | |
DAnIEL |
https://github.com/bioinformatics-leibniz-hki/DAnIEL | No | R/Python/TeX/Shell/Dockerfile/CSS/Other | ITS | DADA2 | ASV/OTU | Sequence composition | SINTAX/rdp | LCA | |
eDNAflow |
https://github.com/mahsa-mousavi/eDNAFlow/ | No | Nextflow/Python/Shell/R | Any | UNOISE3 | zOTU | LULU | Sequence similarity | blast | LCA |
FROGS |
https://frogs.toulouse.inra.fr/ | Yes | HTML/Python/Shell/Other (Galaxy) | Any | DADA2/Swarm | ASV/OTU | Sequence similarity | blast | NA | |
gDAT |
https://github.com/ut-planteco/gDAT/ | No | Python/HTML/Other | ITS/SSU/Any | vsearch | OTU | Sequence similarity | blast | NA | |
JAMP |
https://github.com/VascoElbrecht/JAMP/ | No | R | Any | vsearch | OTU | NA | sequence similarity | usearch_global | NA |
LotuS2 |
https://github.com/hildebra/lotus2/ | Yes (18S) | Perl/R | 16S/18S/23S/28S/ITS | DADA2/uparse/unoise3/cd-hit/vsearch | ASV/OTU | LULU/UNCROSS2/ITSX | Sequence similarity/Sequence composition | Blast/Lambda/usearch/vsearch/rdp/sintax | |
MetaBarFlow |
https://github.com/evaegelyng/MetaBarFlow/ | Yes | R/Python/Shell | Any | DADA2 | ASV | Sequence similarity/Sequence composition | blast/custom | LCA | |
MetaWorks |
https://github.com/terrimporter/MetaWorks/ | Yes | C++/Python/shell | COI/rbcL/ITS/SSU rRNA/12S SSU mtDNA | vsearch | ASV/OTU | Sequence composition | rdp | NA | |
MICCA |
https://github.com/compmetagen/micca/ | No | Python | 16S rRNA/ITS/18S/28S | other | OTU | Sequence composition/Sequence similarity | blast/rdp | ||
MiFish |
https://mitofish.aori.u-tokyo.ac.jp/mifish/ | Yes | Python | 12S Mifish | other | OTU | Sequence similarity | blast | NA | |
OceanOmics-amplicon-nf |
https://github.com/MinderooFoundation/OceanOmics-amplicon-nf | Yes | Nextflow/Python/Groovy/HTML | Any | DADA2 | ASV | Sequence similarity | blast | LCA | |
MJOLNIR |
https://github.com/uit-metabarcoding/MJOLNIR/ | No | R | COI | vsearch/Swarm | OTU | sequence similarity | ecotag | LCA | |
MLI |
Yes | |||||||||
mothur |
https://mothur.org | No | C++/R | 16S/18S/ITS | pre.cluster + chimera tools | OTU | Wang classifier | k-mer / distance | LCA/Consensus | |
NextITS |
https://github.com/vmikk/NextITS/ | No | Nextflow/R/Shell | ITS | vsearch | OTU | Sequence similarity | SH-matcher | mumu | |
nfcore/ampliseq |
https://nf-co.re/ampliseq | Yes | Nextflow | 16S/18S/ITS/COI | DADA2/vsearch | OTU/ASV | sequence composition/sequence similarity | rdp/sintax/blast | None | |
PacMan |
https://github.com/iobis/PacMAN-pipeline/ | Yes | Python/R | Any | DADA2 | ASV | Sequence composition | rdp | LCA | |
PEMA |
https://github.com/hariszaf/pema/ | |||||||||
PipeCraft2 |
https://github.com/pipecraft2/pipecraft/ | Yes | ||||||||
PIPITS |
https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.12399/ | |||||||||
PMiFish |
Yes | |||||||||
QIIME 2 |
https://qiime2.org/ & https://github.com/qiime2/qiime2 | Yes(CHECK) | ||||||||
rainbowbridge |
Yes | |||||||||
SCATA |
https://scata.mykopat.slu.se/ & https://github.com/mikdur/scata | |||||||||
Seed2 |
https://www.biomed.cas.cz/mbu/lbwrf/seed/ | Yes | Pascal | 16S/ITS | expected error filtering | OTU | sequence similarity | blast | None | |
Slim |
https://github.com/yoann-dufresne/SLIM | No | Python | 16S | DADA2-like denoising | OTU/ASV | LULU | sequence similarity | vsearch/IDTAXA | None |
Tourmaline |
https://github.com/aomlomics/tourmaline | Yes | Nextflow | 16S/18S/ITS/COI | DADA2 / Deblur | ASV | sequence composition/sequence similarity | rdp/blast/vsearch | None | |
USEARCH |
https://www.drive5.com/usearch/ | No | C++ | 16S/ITS | UNOISE3/UPARSE | OTU/ASV | sequence composition | SINTAX | None | |
VSEARCH |
https://github.com/torognes/vsearch | Yes | C++ | 16S/ITS | dereplication + chimera+cluster | OTU | sequence composition | SINTAX | None | |
VTAM |
https://github.com/aitgon/vtam | No | Python | COI/16S | replicates + filters | ASV | replicate-validated variants | sequence similarity | blast | None |
This repository was created under the framework of the EU-project MARCO-BOLO. The MARCO-BOLO project is funded by the European Union under the Horizon Europe Programme, Grant Agreement No. 101082021 (MARCO-BOLO). Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Executive Agency (REA). Neither the European Union nor the granting authority can be held responsible for them. UK participants in MARCO-BOLO are supported by the UKRI’s Horizon Europe Guarantee under the Grant No. 10068180 (MS); No. 10063994 (MBA); No. 10048178 (NOC).
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If you have questions or issues, email Mads Reinholdt Jensen (mads.jensen@uit.no) or leave a comment on this repository.