137 tools across 16 categories, all pulled as BioContainer / public images on first use. This page is auto-generated from registry/tools/ by scripts/gen_docs.py.
Ranked by how many papers cited each tool's canonical reference in the last 5 full years — a rough proxy for current adoption. Counts are a lower bound on real use (not everyone cites), and older tools have had longer to accrue totals. Source: Europe PMC.
| # |
Tool |
Category |
Cites 2021–2025 |
Total |
| 1 |
deseq2 |
deg |
52,954 |
73,988 |
| 2 |
star |
rnaseq_align |
29,334 |
42,990 |
| 3 |
starsolo |
single_cell |
29,334 |
42,990 |
| 4 |
bowtie2 |
alignment |
25,726 |
44,452 |
| 5 |
mafft |
comparative_genomics |
19,382 |
31,681 |
| 6 |
edger |
deg |
19,299 |
33,699 |
| 7 |
bwa |
alignment |
18,432 |
37,459 |
| 8 |
bwa_samtools |
alignment |
18,432 |
37,459 |
| 9 |
fastp |
qc |
17,472 |
20,593 |
| 10 |
subread |
rnaseq_align |
15,722 |
21,908 |
| 11 |
bedtools |
alignment |
13,669 |
23,251 |
| 12 |
bcftools |
variant_calling |
10,602 |
12,329 |
| 13 |
samtools |
alignment |
10,602 |
12,329 |
| 14 |
minimap2 |
alignment |
10,300 |
12,728 |
| 15 |
iqtree |
comparative_genomics |
9,889 |
11,566 |
Note: 5 tools show n/a because their registry PMID points to an unrelated paper (author/year mismatch); those references are pending correction. Counts are shown only for PMIDs whose author + year match the cited work.
alignment (7)
| Tool |
Version |
Image |
Citation |
Total cites |
Cites 2021–2025 |
bedtools |
2.31.1 |
quay.io/biocontainers/bedtools:2.31.1--h13024bc_3 |
Quinlan & Hall 2010, PMID 20110278 |
23,251 |
13,669 |
bowtie2 |
2.5.1 |
staphb/bowtie2:2.5.1 |
Langmead & Salzberg 2012, PMID 22388286 |
44,452 |
25,726 |
bwa |
0.7.19 |
quay.io/biocontainers/bwa:0.7.19--h577a1d6_1 |
Li & Durbin 2009, PMID 19451168 |
37,459 |
18,432 |
bwa_mem2 |
2.3 |
quay.io/biocontainers/bwa-mem2:2.3--he70b90d_0 |
Vasimuddin 2019, PMID 31355760 |
n/a |
n/a |
bwa_samtools |
0.7.19 |
quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:f45ad9036aa41bb10f875a330fa877d8869018a1-0 |
Li & Durbin 2009, PMID 19451168 |
37,459 |
18,432 |
minimap2 |
2.31 |
quay.io/biocontainers/minimap2:2.31--h118bc1c_0 |
Li 2018, PMID 29750242 |
12,728 |
10,300 |
samtools |
1.23.1 |
quay.io/biocontainers/samtools:1.23.1--ha83d96e_0 |
Danecek 2021, PMID 33590861 |
12,329 |
10,602 |
assembly (16)
| Tool |
Version |
Image |
Citation |
Total cites |
Cites 2021–2025 |
abyss |
2.3.10 |
quay.io/biocontainers/abyss:2.3.10--h4a2768f_3 |
Jackman 2017, PMID 28232478 |
487 |
311 |
canu |
2.3 |
quay.io/biocontainers/canu:2.3--h3fb4750_2 |
Koren 2017, PMID 28298431 |
5,891 |
3,937 |
flye |
2.9.6 |
quay.io/biocontainers/flye:2.9.6--py313h7fbb527_1 |
Kolmogorov 2019, PMID 30936562 |
4,760 |
3,977 |
hifiasm |
0.25.0 |
quay.io/biocontainers/hifiasm:0.25.0--h5ca1c30_0 |
Cheng 2021, PMID 33526886 |
5,797 |
5,045 |
masurca |
4.1.4 |
quay.io/biocontainers/masurca:4.1.4--ha5bb246_1 |
Zimin 2017, PMID 28130360 |
363 |
224 |
medaka |
2.2.2 |
quay.io/biocontainers/medaka:2.2.2--py312h3050eb1_0 |
Oxford Nanopore Technologies, https://github.com/nanoporetech/medaka |
n/a |
n/a |
megahit |
1.2.9 |
quay.io/biocontainers/megahit:1.2.9--h2e03b76_1 |
Li 2015, PMID 25609793 |
6,760 |
5,259 |
nextdenovo |
2.5.2 |
quay.io/biocontainers/nextdenovo:2.5.2--py311hc29ee83_7 |
Hu 2024, PMID 38671502 |
377 |
303 |
nextpolish |
1.4.1 |
quay.io/biocontainers/nextpolish:1.4.1--h3952c39_7 |
Hu 2020, PMID 31778144 |
994 |
913 |
pilon |
1.24 |
quay.io/biocontainers/pilon:1.24--hdfd78af_0 |
Walker 2014, PMID 25409509 |
7,548 |
5,190 |
racon |
1.5.0 |
quay.io/biocontainers/racon:1.5.0--h21ec9f0_2 |
Vaser 2017, PMID 28100585 |
2,530 |
1,934 |
raven |
1.8.3 |
quay.io/biocontainers/raven-assembler:1.8.3--h5ca1c30_3 |
Vaser & Sikic 2021, PMID 38217213 |
376 |
319 |
shasta |
0.14.0 |
quay.io/biocontainers/shasta:0.14.0--h9948957_0 |
Shafin 2020, PMID 32686750 |
429 |
371 |
spades |
4.3.0 |
staphb/spades:4.3.0 |
Prjibelski 2020, PMID 32559359 |
2,539 |
2,213 |
unicycler |
0.5.1 |
quay.io/biocontainers/unicycler:0.5.1--py312hdcc493e_5 |
Wick 2017, PMID 28594827 |
6,936 |
5,374 |
verkko |
2.3.2 |
quay.io/biocontainers/verkko:2.3.2--hb0edd9e_0 |
Rautiainen 2023, PMID 36797493 |
320 |
279 |
assembly_qc (8)
| Tool |
Version |
Image |
Citation |
Total cites |
Cites 2021–2025 |
bandage |
0.9.0 |
staphb/bandage:0.9.0 |
Wick 2015, PMID 26099265 |
2,243 |
1,637 |
busco |
6.1.0 |
quay.io/biocontainers/busco:6.1.0--pyhdfd78af_1 |
Manni 2021, PMID 34320186 |
5,893 |
5,188 |
checkm2 |
1.1.0 |
quay.io/biocontainers/checkm2:1.1.0--pyh7e72e81_1 |
Chklovski 2023, PMID 37500759 |
1,118 |
799 |
compleasm |
0.2.9 |
quay.io/biocontainers/compleasm:0.2.9--pyhdfd78af_0 |
Huang & Li 2023, PMID 37758247 |
279 |
216 |
genovi |
0.4.3 |
staphb/genovi:0.4.3 |
Cumsille et al. 2023, PMID 37014908 |
87 |
72 |
gfastats |
1.3.11 |
quay.io/biocontainers/gfastats:1.3.11--h077b44d_0 |
Formenti 2022, PMID 35799367 |
1,469 |
1,196 |
merqury |
1.3 |
quay.io/biocontainers/merqury:1.3--hdfd78af_1 |
Rhie 2020, PMID 32928274 |
3,900 |
3,369 |
quast |
5.3.0 |
staphb/quast:5.3.0 |
Mikheenko 2018, PMID 29949969 |
1,209 |
973 |
comparative_genomics (14)
| Tool |
Version |
Image |
Citation |
Total cites |
Cites 2021–2025 |
abricate |
1.4.0 |
staphb/abricate:1.4.0 |
Seemann T, ABRicate, https://github.com/tseemann/abricate |
n/a |
n/a |
cafe5 |
5.1.0 |
quay.io/biocontainers/cafe:5.1.0--h5ca1c30_1 |
Mendes et al. 2021, PMID 33325497 |
n/a |
n/a |
diamond |
2.2.2 |
quay.io/biocontainers/diamond:2.2.2--he361c42_0 |
Buchfink 2021, PMID 33828273 |
4,184 |
3,505 |
fastani |
1.34 |
staphb/fastani:1.34 |
Jain et al. 2018, PMID 30504855 |
4,300 |
3,505 |
fasttree |
2.2.0 |
quay.io/biocontainers/fasttree:2.2.0--h7b50bb2_1 |
Price 2010, PMID 20224823 |
11,440 |
6,433 |
iqtree |
2.4.0 |
staphb/iqtree2:2.4.0 |
Minh et al. 2020, PMID 32011700 |
11,566 |
9,889 |
mafft |
7.526 |
staphb/mafft:7.526 |
Katoh & Standley 2013, PMID 23329690 |
31,681 |
19,382 |
mash |
2.3 |
quay.io/biocontainers/mash:2.3--hb105d93_10 |
Ondov 2016, PMID 27323842 |
2,525 |
1,766 |
muscle |
5.3 |
quay.io/biocontainers/muscle:5.3--h9948957_3 |
Edgar 2022, PMID 36379955 |
751 |
594 |
panaroo |
1.8.0 |
quay.io/biocontainers/panaroo:1.8.0--pyhdfd78af_0 |
Tonkin-Hill 2020, PMID 32698896 |
1,037 |
868 |
roary |
3.13.0 |
staphb/roary:3.13.0 |
Page et al. 2015, PMID 26198102 |
4,547 |
3,111 |
scoary |
1.6.16 |
quay.io/biocontainers/scoary:1.6.16--py_2 |
Brynildsrud 2016, PMID 27887642 |
571 |
406 |
skani |
0.3.2 |
quay.io/biocontainers/skani:0.3.2--h79ce301_0 |
Shaw & Yu 2023, PMID 37735570 |
155 |
114 |
trimal |
1.5.1 |
quay.io/biocontainers/trimal:1.5.1--h9948957_0 |
Capella-Gutierrez 2009, PMID 19505945 |
9,562 |
6,235 |
deg (3)
| Tool |
Version |
Image |
Citation |
Total cites |
Cites 2021–2025 |
deseq2 |
1.50.2 |
quay.io/biocontainers/bioconductor-deseq2:1.50.2--r45ha27e39d_0 |
Love 2014, PMID 25516281 |
73,988 |
52,954 |
edger |
4.8.2 |
quay.io/biocontainers/bioconductor-edger:4.8.2--r45h01b2380_0 |
Robinson 2010, PMID 19910308 |
33,699 |
19,299 |
limma_voom |
3.66.0 |
quay.io/biocontainers/bioconductor-limma:3.66.0--r45h01b2380_0 |
Law 2014, PMID 24485249 |
5,117 |
2,935 |
enrichment (4)
| Tool |
Version |
Image |
Citation |
Total cites |
Cites 2021–2025 |
clusterprofiler |
4.18.4 |
quay.io/biocontainers/bioconductor-clusterprofiler:4.18.4--r45hdfd78af_0 |
Wu 2021, PMID 34557778 |
9,664 |
8,864 |
enrichr |
1.3.1 |
quay.io/biocontainers/gseapy:1.3.1--py311heb3b1e3_0 |
Kuleshov 2016, PMID 27141961 |
8,698 |
6,175 |
gseapy |
1.3.1 |
quay.io/biocontainers/gseapy:1.3.1--py311heb3b1e3_0 |
Fang 2023, PMID 36426870 |
852 |
693 |
topgo |
2.62.0 |
quay.io/biocontainers/bioconductor-topgo:2.62.0--r45hdfd78af_0 |
Alexa & Rahnenfuhrer 2010, https://bioconductor.org/packages/topGO/ |
n/a |
n/a |
epigenomics (8)
| Tool |
Version |
Image |
Citation |
Total cites |
Cites 2021–2025 |
bismark |
0.25.1 |
quay.io/biocontainers/bismark:0.25.1--hdfd78af_0 |
Krueger & Andrews 2011, PMID 21493656 |
4,296 |
2,459 |
deeptools |
3.5.6 |
quay.io/biocontainers/deeptools:3.5.6--pyhdfd78af_0 |
Ramirez et al. 2016, PMID 27079975 |
6,899 |
5,154 |
homer |
5.1 |
quay.io/biocontainers/homer:5.1--pl5321hc52dbad_1 |
Heinz et al. 2010, PMID 20513432 |
11,442 |
6,411 |
macs3 |
3.0.4 |
quay.io/biocontainers/macs3:3.0.4--py310h5a5e57a_0 |
Zhang et al. 2008, PMID 18798982 |
15,567 |
8,561 |
methylkit |
1.36.0 |
quay.io/biocontainers/bioconductor-methylkit:1.36.0--r45ha27e39d_0 |
Akalin et al. 2012, PMID 23034086 |
1,692 |
1,018 |
methylpy |
1.4.7 |
quay.io/biocontainers/methylpy:1.4.7--py39h0ae133c_0 |
Schultz 2015, PMID 26030523 |
559 |
225 |
picard |
3.4.0 |
quay.io/biocontainers/picard:3.4.0--hdfd78af_0 |
Broad Institute, https://broadinstitute.github.io/picard/ |
n/a |
n/a |
tobias |
0.17.3 |
quay.io/biocontainers/tobias:0.17.3--py39hff726c5_1 |
Bentsen et al. 2020, PMID 32848148 |
597 |
529 |
func_annot (10)
| Tool |
Version |
Image |
Citation |
Total cites |
Cites 2021–2025 |
antismash |
8.0.4 |
antismash/standalone:8.0.4 |
Blin 2023, PMID 37140036 |
1,659 |
1,409 |
dbcan |
5.2.9 |
quay.io/biocontainers/dbcan:5.2.9--pyhdfd78af_0 |
Zhang 2018, PMID 29771380 |
1,698 |
1,353 |
dram |
1.5.0 |
quay.io/biocontainers/dram:1.5.0--pyhdfd78af_0 |
Shaffer 2020, PMID 32766782 |
901 |
781 |
eggnog_mapper |
2.1.15 |
quay.io/biocontainers/eggnog-mapper:2.1.15--pyhdfd78af_0 |
Cantalapiedra 2021, PMID 34597405 |
3,499 |
2,925 |
funannotate |
1.8.17 |
quay.io/biocontainers/funannotate:1.8.17--pyhdfd78af_5 |
Palmer & Stajich 2020, funannotate (Zenodo) |
n/a |
n/a |
gecco |
0.10.3 |
quay.io/biocontainers/gecco:0.10.3--pyhdfd78af_1 |
Larralde 2021, GECCO (bioRxiv 10.1101/2021.05.03.442509) |
n/a |
n/a |
gtdbtk |
2.7.2 |
quay.io/biocontainers/gtdbtk:2.7.2--pyhdfd78af_0 |
Chaumeil 2022, PMID 36218463 |
1,547 |
1,217 |
interproscan |
5.59_91.0 |
quay.io/biocontainers/interproscan:5.59_91.0--hec16e2b_1 |
Blum 2021, PMID 33156333 |
1,761 |
1,654 |
kofamscan |
1.3.0 |
quay.io/biocontainers/kofamscan:1.3.0--hdfd78af_2 |
Aramaki 2020, PMID 31742321 |
1,454 |
1,237 |
pfam_scan |
1.6 |
quay.io/biocontainers/pfam_scan:1.6--hdfd78af_5 |
Mistry 2021, PMID 33125078 |
4,934 |
4,535 |
| Tool |
Version |
Image |
Citation |
Total cites |
Cites 2021–2025 |
bracken |
3.1 |
quay.io/biocontainers/bracken:3.1--h9948957_0 |
Lu et al. 2017, PMID 28655956 |
n/a |
n/a |
humann3 |
3.9 |
quay.io/biocontainers/humann:3.9--py312hdfd78af_0 |
Beghini et al. 2021, PMID 33944776 |
1,771 |
1,562 |
kneaddata |
0.12.4 |
quay.io/biocontainers/kneaddata:0.12.4--pyhdfd78af_0 |
McIver et al. 2018, PMID 31616210 |
n/a |
n/a |
kraken2 |
2.17.1 |
quay.io/biocontainers/kraken2:2.17.1--pl5321h077b44d_0 |
Wood et al. 2019, PMID 31779668 |
5,146 |
4,364 |
krona |
2.8.1 |
staphb/krona:2.8.1 |
Ondov 2011, PMID 21961884 |
1,393 |
768 |
lefse |
1.1.2 |
quay.io/biocontainers/lefse:1.1.2--pyhdfd78af_0 |
Segata et al. 2011, PMID 21702898 |
11,429 |
7,376 |
maxbin2 |
2.2.7 |
quay.io/biocontainers/maxbin2:2.2.7--h503566f_8 |
Wu 2016, PMID 26515820 |
2,120 |
1,598 |
metabat2 |
2.18 |
quay.io/biocontainers/metabat2:2.18--h38e344b_2 |
Kang 2019, PMID 31388474 |
2,979 |
2,525 |
metaphlan4 |
4.2.4 |
quay.io/biocontainers/metaphlan:4.2.4--pyhdfd78af_0 |
Blanco-Miguez et al. 2023, PMID 36823356 |
1,083 |
847 |
sourmash |
4.9.4 |
quay.io/biocontainers/sourmash:4.9.4--hdfd78af_0 |
Brown & Irber 2016, sourmash (JOSS 10.21105/joss.00027) |
n/a |
n/a |
proteomics (9)
| Tool |
Version |
Image |
Citation |
Total cites |
Cites 2021–2025 |
comet |
2026.01.1 |
quay.io/biocontainers/comet-ms:2026011--h9ee0642_0 |
Eng 2013, PMID 23148064 |
1,305 |
741 |
fragpipe ⚠️ deprecated |
22.0 |
fcyu/fragpipe:22.0 |
Yu et al. 2020, PMID 33338430 |
n/a |
n/a |
maxquant ⚠️ deprecated |
2.4.14.0 |
quay.io/biocontainers/maxquant:2.4.14.0--hdfd78af_0 |
Cox & Mann 2008, PMID 19029910 |
12,826 |
5,690 |
msconvert |
3.0.24238 |
chambm/pwiz-skyline-i-agree-to-the-vendor-licenses:latest |
Chambers et al. 2012, PMID 23051804 |
3,272 |
2,078 |
msfragger ⚠️ deprecated |
4.1 |
fcyu/msfragger:4.1 |
Kong et al. 2017, PMID 28394336 |
2,077 |
1,651 |
msgf_plus |
2024.03.26 |
quay.io/biocontainers/msgf_plus:2024.03.26--hdfd78af_0 |
Kim 2014, PMID 25358478 |
905 |
449 |
openms |
3.5.0 |
quay.io/biocontainers/openms:3.5.0--h78fb946_0 |
Rost 2016, PMID 27575624 |
513 |
321 |
percolator |
3.9 |
quay.io/biocontainers/percolator:3.9--h0f90025_0 |
Kall et al. 2007, PMID 17952086 |
1,996 |
931 |
xtandem |
15.12.15.2 |
quay.io/biocontainers/xtandem:15.12.15.2--h4464bbb_11 |
Craig & Beavis 2004, PMID 14976030 |
1,938 |
323 |
qc (9)
| Tool |
Version |
Image |
Citation |
Total cites |
Cites 2021–2025 |
cutadapt |
5.2 |
quay.io/biocontainers/cutadapt:5.2--py312hfabe715_2 |
Martin 2011, doi:10.14806/ej.17.1.200 |
n/a |
n/a |
fastp |
1.3.6 |
quay.io/biocontainers/fastp:1.3.6--h43da1c4_0 |
Chen 2018, PMID 30423086 |
20,593 |
17,472 |
fastqc |
0.12.1 |
quay.io/biocontainers/fastqc:0.12.1--hdfd78af_0 |
Andrews S, 2010 (Babraham Bioinformatics) |
n/a |
n/a |
filtlong |
0.3.1 |
quay.io/biocontainers/filtlong:0.3.1--h077b44d_0 |
Wick 2021 (github.com/rrwick/Filtlong) |
n/a |
n/a |
multiqc |
1.35 |
quay.io/biocontainers/multiqc:1.35--pyhdfd78af_1 |
Ewels 2016, PMID 27312411 |
8,254 |
6,543 |
nanoplot |
1.47.1 |
quay.io/biocontainers/nanoplot:1.47.1--pyhdfd78af_0 |
De Coster 2023, PMID 37171891 |
622 |
459 |
seqkit |
2.13.0 |
quay.io/biocontainers/seqkit:2.13.0--he881be0_0 |
Shen 2016, PMID 27706213 |
2,637 |
2,208 |
seqtk |
r93 |
quay.io/biocontainers/seqtk:r93--0 |
Li, seqtk (github.com/lh3/seqtk) |
n/a |
n/a |
trimgalore |
0.6.11 |
quay.io/biocontainers/trim-galore:0.6.11--hdfd78af_0 |
Krueger 2015, https://github.com/FelixKrueger/TrimGalore |
n/a |
n/a |
repeat (3)
| Tool |
Version |
Image |
Citation |
Total cites |
Cites 2021–2025 |
earlgrey |
7.2.6 |
quay.io/biocontainers/earlgrey:7.2.6--hc52dbad_0 |
Baril 2024, PMID 38577785 |
185 |
129 |
repeatmasker |
4.1.7 |
dfam/tetools:1.89 |
Smit 2015 (repeatmasker.org) |
n/a |
n/a |
repeatmodeler |
2.0.5 |
dfam/tetools:1.89 |
Flynn 2020, PMID 32300014 |
3,195 |
2,804 |
rnaseq_align (8)
| Tool |
Version |
Image |
Citation |
Total cites |
Cites 2021–2025 |
hisat2 |
2.2.2 |
quay.io/biocontainers/hisat2:2.2.2--h503566f_0 |
Kim 2019, PMID 31375807 |
11,302 |
9,746 |
htseq |
2.1.2 |
quay.io/biocontainers/htseq:2.1.2--py311h483b626_2 |
Anders 2015, PMID 25260700 |
17,232 |
9,300 |
kallisto |
0.52.0 |
quay.io/biocontainers/kallisto:0.52.0--h13ff97a_0 |
Bray 2016, PMID 27043002 |
8,010 |
5,338 |
rsem |
1.3.3 |
quay.io/biocontainers/rsem:1.3.3--pl5321h077b44d_12 |
Li & Dewey 2011, PMID 21816040 |
16,480 |
9,518 |
salmon |
2.4.1 |
quay.io/biocontainers/salmon:2.4.1--hfa8f182_0 |
Patro 2017, PMID 28263959 |
10,005 |
7,575 |
star |
2.7.11b |
quay.io/biocontainers/star:2.7.11b--h43eeafb_0 |
Dobin 2013, PMID 23104886 |
42,990 |
29,334 |
stringtie |
3.0.3 |
quay.io/biocontainers/stringtie:3.0.3--h29c0135_0 |
Pertea 2015, PMID 25690850 |
10,338 |
7,746 |
subread |
2.1.1 |
quay.io/biocontainers/subread:2.1.1--h577a1d6_0 |
Liao 2014, PMID 24227677 |
21,908 |
15,722 |
single_cell (9)
| Tool |
Version |
Image |
Citation |
Total cites |
Cites 2021–2025 |
bustools |
0.45.1 |
quay.io/biocontainers/bustools:0.45.1--h6f0a7f7_0 |
Melsted 2019, PMID 31073610 |
122 |
108 |
cellranger |
9.0.1 |
litd/docker-cellranger:v9.0.1 |
Zheng et al. 2017, PMID 28091601 |
5,838 |
4,132 |
harmony |
2.0.0 |
quay.io/biocontainers/harmonypy:2.0.0--py310hd766df8_1 |
Korsunsky 2019, PMID 31740819 |
8,090 |
6,797 |
kb_python |
0.28.2 |
quay.io/biocontainers/kb-python:0.28.2--pyhdfd78af_2 |
Melsted 2021, PMID 33795888 |
333 |
312 |
monocle3 |
1.4.26 |
quay.io/biocontainers/r-monocle3:1.4.26--r44h9948957_0 |
Cao et al. 2019, PMID 30787392 |
430 |
373 |
scanpy |
1.12.2 |
ghcr.io/hope9901/bioflow-scanpy:1.12.2 |
Wolf et al. 2018, PMID 29409532 |
6,990 |
5,691 |
scrublet |
0.2.3 |
quay.io/biocontainers/scrublet:0.2.3--pyh5e36f6f_1 |
Wolock 2019, PMID 30954476 |
2,287 |
1,874 |
seurat |
5.5.1 |
satijalab/seurat:5.5.1 |
Hao et al. 2024, PMID 37231261 |
4,025 |
2,901 |
starsolo |
2.7.11b |
quay.io/biocontainers/star:2.7.11b--h43eeafb_0 |
Dobin et al. 2013, PMID 23104886 |
42,990 |
29,334 |
struct_annot (10)
| Tool |
Version |
Image |
Citation |
Total cites |
Cites 2021–2025 |
augustus |
3.5.0 |
quay.io/biocontainers/augustus:3.5.0--pl5321h9716f88_9 |
Stanke 2008, PMID 18218656 |
2,034 |
1,276 |
bakta |
1.12.0 |
quay.io/biocontainers/bakta:1.12.0--pyhdfd78af_0 |
Schwengers 2021, PMID 34739369 |
986 |
797 |
braker3 |
3.1.1 |
teambraker/braker3:v3.1.1 |
Gabriel 2024, PMID 38866550 |
526 |
376 |
dfast |
1.4.1 |
quay.io/biocontainers/dfast:1.4.1--h7f5d12c_0 |
Tanizawa 2018, PMID 29106469 |
1,038 |
768 |
glimmerhmm |
3.0.4 |
quay.io/biocontainers/glimmerhmm:3.0.4--pl5321h503566f_10 |
Majoros 2004, PMID 15145805 |
1,527 |
966 |
liftoff |
1.6.3 |
quay.io/biocontainers/liftoff:1.6.3--pyhdfd78af_0 |
Shumate & Salzberg 2021, PMID 33320174 |
778 |
677 |
prodigal |
2.6.3 |
quay.io/biocontainers/prodigal:2.6.3--h577a1d6_11 |
Hyatt 2010, PMID 20211023 |
9,372 |
5,543 |
prokka |
1.14.6 |
staphb/prokka:1.14.6 |
Seemann 2014, PMID 24642063 |
14,770 |
9,782 |
snap |
2017-03-01 |
quay.io/biocontainers/snap:2017_03_01--h7b50bb2_0 |
Korf 2004, PMID 15144565 |
2,583 |
1,451 |
trnascan_se |
2.0.13 |
quay.io/biocontainers/trnascan-se:2.0.13--pl5321hab16a5f_0 |
Chan 2021, PMID 34417604 |
1,458 |
1,229 |
variant_calling (9)
| Tool |
Version |
Image |
Citation |
Total cites |
Cites 2021–2025 |
bcftools |
1.24 |
quay.io/biocontainers/bcftools:1.24--h487d631_1 |
Danecek 2021, PMID 33590861 |
12,329 |
10,602 |
deepvariant |
1.10.0 |
google/deepvariant:1.10.0 |
Poplin 2018, PMID 30247488 |
1,242 |
976 |
delly |
2.5.1 |
quay.io/biocontainers/delly:2.5.1--h3752d28_0 |
Rausch 2012, PMID 22962449 |
1,940 |
1,091 |
ensembl_vep |
116.0 |
quay.io/biocontainers/ensembl-vep:116.0--pl5321h2a3209d_0 |
McLaren 2016, PMID 27268795 |
6,391 |
4,495 |
freebayes |
1.3.10 |
quay.io/biocontainers/freebayes:1.3.10--hbefcdb2_0 |
Garrison & Marth 2012, arXiv:1207.3907 |
n/a |
n/a |
gatk4 |
4.6.2.0 |
quay.io/biocontainers/gatk4:4.6.2.0--py310hdfd78af_1 |
McKenna 2010, PMID 20644199 |
16,862 |
8,020 |
glnexus |
1.4.1 |
quay.io/biocontainers/glnexus:1.4.1--h40d77a6_0 |
Yun 2021, PMID 33399819 |
191 |
166 |
snpeff |
5.4.0c |
quay.io/biocontainers/snpeff:5.4.0c--hdfd78af_0 |
Cingolani 2012, PMID 22728672 |
9,555 |
5,432 |
vcftools |
0.1.17 |
quay.io/biocontainers/vcftools:0.1.17--pl5321h077b44d_0 |
Danecek 2011, PMID 21653522 |
12,172 |
7,484 |