A curated cohort of metagenomics / microbial-genomics tools spanning the whole toolchain — read QC, alignment, assembly, MAG recovery, gene prediction & functional annotation, taxonomic and amplicon profiling, viral, plasmid and strain-level analysis, biosynthetic-gene-cluster mining, phylogenetics and AMR — each tracked by the full citation history of its method paper. The curves show adoption growing, who leads in any given year, and where the crown changes hands — exact citing-paper counts from the OpenAlex citation graph, re-counted weekly.
Trimmomatic
most-cited · 65K citations
145
tools tracked
17
tool groups
2004–2025
citation years
Read QC & preprocessing · annual citations
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Y axis
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Read QC & preprocessing · GitHub stars
fastp
2.4K ★
Cutadapt
582 ★
Trimmomatic
308 ★
SortMeRNA
295 ★
NanoPack
291 ★
PRINSEQ
SourceForge
Read QC & preprocessing · maintenance · last commit
fastp
active · this month
Cutadapt
active · this month
SortMeRNA
active · this month
Trimmomatic
active · this month
NanoPack
stale · 3.1 yr ago
PRINSEQ
unknown
Software health, not citations: GitHub/GitLab stars and last-commit date for each tool’s canonical source repo, as a point-in-time snapshot (2026-06-30). Bars in the last-commit chart show how recently each repo was touched — active, stale, archived or gone. Star bars are tinted to match each tool’s citation line above.
Read alignment & mapping · annual citations
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Y axis
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Read alignment & mapping · GitHub stars
minimap2
2.2K ★
SAMtools
1.9K ★
BWA
1.8K ★
Salmon
901 ★
Bowtie 2
795 ★
HISAT2
539 ★
Read alignment & mapping · maintenance · last commit
Salmon
active · this month
SAMtools
active · this month
BWA
active · this month
Bowtie 2
active · this month
minimap2
active · 1 mo ago
HISAT2
active · 5 mo ago
Software health, not citations: GitHub/GitLab stars and last-commit date for each tool’s canonical source repo, as a point-in-time snapshot (2026-06-30). Bars in the last-commit chart show how recently each repo was touched — active, stale, archived or gone. Star bars are tinted to match each tool’s citation line above.
Metagenome assembly · annual citations
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Y axis
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Metagenome assembly · GitHub stars
SPAdes
947 ★
metaSPAdes
947 ★
Flye
941 ★
metaFlye
941 ★
MEGAHIT
719 ★
Canu
701 ★
Unicycler
645 ★
IDBA-UD
132 ★
OPERA-MS
102 ★
Ray Meta
68 ★
MetaVelvet
15 ★
MOCAT
web
MetaHipMer
Bitbucket
Metagenome assembly · maintenance · last commit
Canu
active · this month
SPAdes
active · this month
metaSPAdes
active · this month
Flye
active · 3 mo ago
metaFlye
active · 3 mo ago
MEGAHIT
active · 8 mo ago
Unicycler
stale · 1.9 yr ago
OPERA-MS
stale · 2.0 yr ago
IDBA-UD
stale · 3.0 yr ago
Ray Meta
stale · 8.9 yr ago
MetaVelvet
stale · 14 yr ago
MOCAT
unknown
MetaHipMer
unknown
Software health, not citations: GitHub/GitLab stars and last-commit date for each tool’s canonical source repo, as a point-in-time snapshot (2026-06-30). Bars in the last-commit chart show how recently each repo was touched — active, stale, archived or gone. Star bars are tinted to match each tool’s citation line above.
Binning & MAG recovery · annual citations
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Y axis
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Binning & MAG recovery · GitHub stars
MetaWRAP
472 ★
VAMB
328 ★
DAS Tool
174 ★
SemiBin2
164 ★
SemiBin
164 ★
CONCOCT
139 ★
COMEBin
78 ★
GraphMB
36 ★
MetaBAT 2
Bitbucket
MaxBin 2.0
SourceForge
Binning & MAG recovery · maintenance · last commit
SemiBin2
active · this month
SemiBin
active · this month
VAMB
active · 2 mo ago
DAS Tool
stale · 2.2 yr ago
COMEBin
stale · 2.3 yr ago
GraphMB
stale · 2.6 yr ago
MetaWRAP
stale · 2.9 yr ago
CONCOCT
stale · 6.3 yr ago
MetaBAT 2
unknown
MaxBin 2.0
unknown
Software health, not citations: GitHub/GitLab stars and last-commit date for each tool’s canonical source repo, as a point-in-time snapshot (2026-06-30). Bars in the last-commit chart show how recently each repo was touched — active, stale, archived or gone. Star bars are tinted to match each tool’s citation line above.
MAG quality & curation · annual citations
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Y axis
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MAG quality & curation · GitHub stars
CheckM
410 ★
dRep
347 ★
CheckM2
268 ★
MAG quality & curation · maintenance · last commit
dRep
active · this month
CheckM
active · 4 mo ago
CheckM2
active · 1.3 yr ago
Software health, not citations: GitHub/GitLab stars and last-commit date for each tool’s canonical source repo, as a point-in-time snapshot (2026-06-30). Bars in the last-commit chart show how recently each repo was touched — active, stale, archived or gone. Star bars are tinted to match each tool’s citation line above.
Gene prediction & annotation · annual citations
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Y axis
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Gene prediction & annotation · GitHub stars
Prokka
985 ★
Bakta
656 ★
Prodigal
542 ★
DFAST
86 ★
MetaGeneMark
web
FragGeneScan
SourceForge
Gene prediction & annotation · maintenance · last commit
DFAST
active · this month
Bakta
active · 2 mo ago
Prokka
active · 6 mo ago
Prodigal
stale · 2.4 yr ago
MetaGeneMark
unknown
FragGeneScan
unknown
Software health, not citations: GitHub/GitLab stars and last-commit date for each tool’s canonical source repo, as a point-in-time snapshot (2026-06-30). Bars in the last-commit chart show how recently each repo was touched — active, stale, archived or gone. Star bars are tinted to match each tool’s citation line above.
Hover a line, or focus a legend item, to see exact citation values. Click legend items to hide or show tools.
Functional & pathway annotation · GitHub stars
eggNOG-mapper v2
749 ★
PICRUSt2
392 ★
InterProScan 5
385 ★
DRAM
333 ★
HUMAnN 3
247 ★
dbCAN2
166 ★
KofamScan
100 ★
Functional & pathway annotation · maintenance · last commit
InterProScan 5
active · this month
HUMAnN 3
active · this month
DRAM
active · this month
eggNOG-mapper v2
active · 1 mo ago
PICRUSt2
active · 7 mo ago
dbCAN2
active · 1.2 yr ago
KofamScan
stale · 3.1 yr ago
Software health, not citations: GitHub/GitLab stars and last-commit date for each tool’s canonical source repo, as a point-in-time snapshot (2026-06-30). Bars in the last-commit chart show how recently each repo was touched — active, stale, archived or gone. Star bars are tinted to match each tool’s citation line above.
Taxonomic profiling & classification · maintenance · last commit
sourmash
active · this month
DIAMOND
active · this month
Kraken 2
active · this month
CLARK
active · this month
MMseqs2 taxonomy
active · this month
mOTUs2
active · this month
ganon
active · this month
Kaiju
active · this month
MetaPhlAn2
active · this month
MetaPhlAn
active · this month
MetaPhlAn 4
active · this month
Centrifuger
active · this month
GTDB-Tk
active · 1 mo ago
Centrifuge
active · 3 mo ago
Metabuli
active · 3 mo ago
CAT/BAT
active · 3 mo ago
Bracken
active · 4 mo ago
sylph
active · 5 mo ago
MEGAN CE
stale · 2.0 yr ago
KrakenUniq
stale · 2.4 yr ago
Kraken
stale · 4.8 yr ago
PhyloSift
stale · 10 yr ago
Software health, not citations: GitHub/GitLab stars and last-commit date for each tool’s canonical source repo, as a point-in-time snapshot (2026-06-30). Bars in the last-commit chart show how recently each repo was touched — active, stale, archived or gone. Star bars are tinted to match each tool’s citation line above.
Hover a line, or focus a legend item, to see exact citation values. Click legend items to hide or show tools.
Amplicon & marker-gene profiling · GitHub stars
VSEARCH
750 ★
phyloseq
651 ★
DADA2
552 ★
QIIME 2
527 ★
mothur
278 ★
Deblur
99 ★
UPARSE
web
Amplicon & marker-gene profiling · maintenance · last commit
VSEARCH
active · this month
QIIME 2
active · this month
phyloseq
active · 4 mo ago
DADA2
active · 5 mo ago
mothur
active · 6 mo ago
Deblur
active · 1.3 yr ago
UPARSE
unknown
Software health, not citations: GitHub/GitLab stars and last-commit date for each tool’s canonical source repo, as a point-in-time snapshot (2026-06-30). Bars in the last-commit chart show how recently each repo was touched — active, stale, archived or gone. Star bars are tinted to match each tool’s citation line above.
Viral discovery & viromics · annual citations
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Y axis
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Viral discovery & viromics · GitHub stars
geNomad
318 ★
VirSorter2
293 ★
VIBRANT
197 ★
DeepVirFinder
154 ★
VirFinder
138 ★
VirSorter
101 ★
Cenote-Taker 2
56 ★
MARVEL
51 ★
PhaGCN2
35 ★
Seeker
33 ★
PhaTYP
19 ★
PHASTER
web
CheckV
Bitbucket
vConTACT2
Bitbucket
iPHoP
Bitbucket
Viral discovery & viromics · maintenance · last commit
DeepVirFinder
active · 2 mo ago
geNomad
active · 3 mo ago
PhaGCN2
active · 1.0 yr ago
VirSorter2
stale · 1.6 yr ago
PhaTYP
stale · 1.6 yr ago
MARVEL
stale · 2.2 yr ago
VIBRANT
stale · 2.2 yr ago
Cenote-Taker 2
stale · 2.4 yr ago
Seeker
stale · 5.0 yr ago
VirSorter
stale · 5.7 yr ago
VirFinder
stale · 6.2 yr ago
PHASTER
unknown
CheckV
unknown
vConTACT2
unknown
iPHoP
unknown
Software health, not citations: GitHub/GitLab stars and last-commit date for each tool’s canonical source repo, as a point-in-time snapshot (2026-06-30). Bars in the last-commit chart show how recently each repo was touched — active, stale, archived or gone. Star bars are tinted to match each tool’s citation line above.
Plasmid recovery & typing · annual citations
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Y axis
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Plasmid recovery & typing · GitHub stars
plasmidSPAdes
947 ★
MOB-suite
177 ★
Platon
122 ★
PlasFlow
111 ★
Recycler
58 ★
Plasmer
50 ★
PPR-Meta
44 ★
SCAPP
37 ★
PLASMe
35 ★
PlasClass
33 ★
PlasmidFinder
32 ★
COPLA
28 ★
Deeplasmid
21 ★
gplas
4 ★
cBar
web
Plasmid recovery & typing · maintenance · last commit
plasmidSPAdes
active · this month
Platon
active · 1 mo ago
MOB-suite
active · 1.2 yr ago
Deeplasmid
stale · 1.8 yr ago
PlasClass
stale · 2.0 yr ago
PLASMe
stale · 2.2 yr ago
PlasmidFinder
stale · 2.7 yr ago
gplas
stale · 3.2 yr ago
Plasmer
stale · 3.2 yr ago
SCAPP
stale · 3.3 yr ago
COPLA
stale · 5.0 yr ago
PlasFlow
stale · 5.0 yr ago
Recycler
stale · 5.2 yr ago
PPR-Meta
stale · 5.2 yr ago
cBar
unknown
Software health, not citations: GitHub/GitLab stars and last-commit date for each tool’s canonical source repo, as a point-in-time snapshot (2026-06-30). Bars in the last-commit chart show how recently each repo was touched — active, stale, archived or gone. Star bars are tinted to match each tool’s citation line above.
Strain-level resolution · annual citations
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Y axis
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Strain-level resolution · GitHub stars
StrainPhlAn
413 ★
inStrain
190 ★
MIDAS
135 ★
DESMAN
72 ★
Strainberry
52 ★
StrainGE
41 ★
Strain-level resolution · maintenance · last commit
StrainPhlAn
active · this month
inStrain
active · 4 mo ago
StrainGE
stale · 1.7 yr ago
MIDAS
stale · 2.7 yr ago
Strainberry
stale · 4.6 yr ago
DESMAN
stale · 6.0 yr ago
Software health, not citations: GitHub/GitLab stars and last-commit date for each tool’s canonical source repo, as a point-in-time snapshot (2026-06-30). Bars in the last-commit chart show how recently each repo was touched — active, stale, archived or gone. Star bars are tinted to match each tool’s citation line above.
Biosynthetic gene clusters · annual citations
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Y axis
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Biosynthetic gene clusters · GitHub stars
antiSMASH
257 ★
BiG-SCAPE
172 ★
DeepBGC
158 ★
BiG-SLiCE
101 ★
PRISM
9 ★
Biosynthetic gene clusters · maintenance · last commit
antiSMASH
active · this month
BiG-SCAPE
active · 3 mo ago
BiG-SLiCE
active · 11 mo ago
DeepBGC
stale · 2.6 yr ago
PRISM
stale · 5.4 yr ago
Software health, not citations: GitHub/GitLab stars and last-commit date for each tool’s canonical source repo, as a point-in-time snapshot (2026-06-30). Bars in the last-commit chart show how recently each repo was touched — active, stale, archived or gone. Star bars are tinted to match each tool’s citation line above.
Phylogenetics & alignment · annual citations
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Y axis
Hover a line, or focus a legend item, to see exact citation values. Click legend items to hide or show tools.
Phylogenetics & alignment · GitHub stars
RAxML
348 ★
IQ-TREE 2
333 ★
MUSCLE
284 ★
trimAl
263 ★
FastTree 2
39 ★
MAFFT 7
web
Phylogenetics & alignment · maintenance · last commit
trimAl
active · this month
FastTree 2
active · 2 mo ago
MUSCLE
active · 2 mo ago
IQ-TREE 2
active · 4 mo ago
RAxML
active · 1.3 yr ago
MAFFT 7
unknown
Software health, not citations: GitHub/GitLab stars and last-commit date for each tool’s canonical source repo, as a point-in-time snapshot (2026-06-30). Bars in the last-commit chart show how recently each repo was touched — active, stale, archived or gone. Star bars are tinted to match each tool’s citation line above.
Isolate AMR calling · annual citations
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Y axis
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Isolate AMR calling · GitHub stars
AMRFinderPlus
371 ★
ARIBA
186 ★
SRST2
148 ★
Kleborate
141 ★
Mykrobe
118 ★
PointFinder
Bitbucket
Isolate AMR calling · maintenance · last commit
AMRFinderPlus
active · this month
Kleborate
active · this month
Mykrobe
active · 3 mo ago
ARIBA
stale · 2.7 yr ago
SRST2
stale · 5.0 yr ago
PointFinder
unknown
Software health, not citations: GitHub/GitLab stars and last-commit date for each tool’s canonical source repo, as a point-in-time snapshot (2026-06-30). Bars in the last-commit chart show how recently each repo was touched — active, stale, archived or gone. Star bars are tinted to match each tool’s citation line above.
Hover a line, or focus a legend item, to see exact citation values. Click legend items to hide or show tools.
Metagenomic resistome profiling · GitHub stars
DeepARG
60 ★
AMR++
53 ★
ARGs-OAP
46 ★
fARGene
36 ★
ShortBRED
31 ★
PathoFact
0 ★
Metagenomic resistome profiling · maintenance · last commit
AMR++
active · this month
DeepARG
active · 2 mo ago
PathoFact
active · 4 mo ago
ShortBRED
active · 1.4 yr ago
fARGene
stale · 3.6 yr ago
ARGs-OAP
stale · 5.4 yr ago
Software health, not citations: GitHub/GitLab stars and last-commit date for each tool’s canonical source repo, as a point-in-time snapshot (2026-06-30). Bars in the last-commit chart show how recently each repo was touched — active, stale, archived or gone. Star bars are tinted to match each tool’s citation line above.
AMR reference databases · annual citations
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Y axis
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AMR reference databases · GitHub stars
ResFinder
10 ★
Resfams
3 ★
CARD
web
ARG-ANNOT
web
BacMet
web
MEGARes
web
AMR reference databases · maintenance · last commit
ResFinder
stale · 2.6 yr ago
Resfams
stale · 8.3 yr ago
CARD
unknown
ARG-ANNOT
unknown
BacMet
unknown
MEGARes
unknown
Software health, not citations: GitHub/GitLab stars and last-commit date for each tool’s canonical source repo, as a point-in-time snapshot (2026-06-30). Bars in the last-commit chart show how recently each repo was touched — active, stale, archived or gone. Star bars are tinted to match each tool’s citation line above.
Use cumulative view for long-run adoption and annual view for citation momentum; log scale makes smaller tools readable without changing the counts. Counts are annual OpenAlex cited-by tallies and reflect all uses of each paper, not only use inside the selected workflow; broad tools can therefore look larger than workflow-specific methods. The still-filling current year (2026) is omitted from the lines.
Development activity vs ongoing use
Each dot is one of 126 curated tools with a datable code repository (19 web-only / SourceForge tools without a public commit date aren't shown). Higher means more cited in 2025, the latest complete year (log scale); further left means more recently updated (square-root scale). Filled dots are actively maintained — a commit within the last 18 months. The upper-left gathers the field's well-kept, widely-used staples: fastp, SAMtools, DADA2, SPAdes, Prokka, DIAMOND and more, updated regularly and cited thousands of times a year. Maintenance and citations are only loosely linked (Spearman ρ ≈ −0.46): a citation counts every paper that mentions a method, so a quieter commit history does not mean a tool is unused or unmaintained — many stable, widely-relied-on tools rarely need new commits, and development sometimes moves to mirrors this snapshot can't see. Source: OpenAlex citation graph + GitHub/GitLab activity, as of 2026-11-09.
Who led each year (2004–2025)
MUSCLE
’04–’20
BWA
2021
SAMtools
’22–’24
Trimmomatic
2025
The most-cited tool of the cohort in each calendar year, by cumulative citations. The crown started with early assemblers and now compares read-QC, alignment, assembly, genome-recovery, annotation, profiling, viral, plasmid, strain and AMR papers side by side — a 4-way hand-off across 22 years.
MetricCitations to each tool’s canonical method paper, counted by the citing paper’s publication year
MeasurementAnnual cited-by counts from OpenAlex (cites: grouped by year when available; counts_by_year fallback when the grouped endpoint is budget-limited)
A curated cohort of the read-QC, alignment, assembly, genome-recovery, annotation, functional, taxonomic, amplicon, viral, plasmid, strain-resolution, gene-cluster, phylogenetics and AMR methods a sequencing facility actually chooses between, each tracked by the full citation history of its method paper — re-counted weekly straight from the OpenAlex citation graph. Only the published method papers and their public citation counts are used. · back to all research data