ABRicate ![docker pulls](https://camo.githubusercontent.com/825613da17aaaf192503af2ffc7c415653d2fe03231417aaba031678b4d80565/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f6162726963617465) |
|
https://github.com/tseemann/abricate |
any2fasta ![docker pulls](https://camo.githubusercontent.com/950f6d6a1a379192f05a810cf1b23566fa090230308705b8cb6bd2e4b3171088/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f616e79326661737461) |
|
https://github.com/tseemann/any2fasta |
ARIBA ![docker pulls](https://camo.githubusercontent.com/2ae737c7f47966fd6e94df2ac10229b31bdcaae3ba48b88d6ee512dba3c0211d/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f6172696261) |
|
https://github.com/sanger-pathogens/ariba |
artic-ncov2019 ![docker pulls](https://camo.githubusercontent.com/4d41af7a331b528667bb03bed68feeb8038b086f224eaa3c246ffa921c416d6a/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f61727469632d6e636f7632303139) |
|
https://github.com/artic-network/fieldbioinformatics |
artic-ncov2019-epi2me ![docker pulls](https://camo.githubusercontent.com/ff86f41be4ac57ec5a8a8394bd5dc1a63bfa4cdaf38a72dce11d10c9239e2417/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f61727469632d6e636f76323031392d657069326d65) |
|
https://github.com/epi2me-labs/wf-artic |
artic-ncov2019-medaka ![docker pulls](https://camo.githubusercontent.com/1c6a4b95bac06e92dbdc3901a2bcfab00829cccc99aeae969a9d360e829da16a/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f61727469632d6e636f76323031392d6d6564616b61) |
|
https://github.com/artic-network/artic-ncov2019 |
artic-ncov2019-nanopolish ![docker pulls](https://camo.githubusercontent.com/6e5561c7dccd9ec4c83595b9753f8ed4c6856b3bf541a924d88e3775fe907ca3/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f61727469632d6e636f76323031392d6e616e6f706f6c697368) |
|
https://github.com/artic-network/artic-ncov2019 |
Augur ![docker pulls](https://camo.githubusercontent.com/e2d8deebfbaf4ae105dd5988893a8acde216783681852e161629231b4957524f/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f6175677572) |
- 6.3.0
- 7.0.2
- 8.0.0
- 9.0.0
- 16.0.3
|
https://github.com/nextstrain/augur |
Auspice ![docker pulls](https://camo.githubusercontent.com/27a54d848dc4d2baad3918764ea9dc188ea34e6fcfec8e9c5a0e15072896af74/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f61757370696365) |
|
https://github.com/nextstrain/auspice |
BBTools ![docker pulls](https://camo.githubusercontent.com/af3c15ace85eba9f37a58a937c42b365233f1059361a53933b2993418179bcc7/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f6262746f6f6c73) |
- 38.76
- 38.86
- 38.95
- 38.96
- 38.97
- 38.98
- 38.99
- 39.00
- 39.01
|
https://jgi.doe.gov/data-and-tools/bbtools/ |
bcftools ![docker pulls](https://camo.githubusercontent.com/3edc00a3c9f5768980cf9be95db3e9ac5dbdd2b54613ab68aadee17d1ba78f9a/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f626366746f6f6c73) |
- 1.10.2
- 1.11
- 1.12
- 1.13
- 1.14
- 1.15
- 1.16
- 1.17
|
https://github.com/samtools/bcftools |
bedtools ![docker pulls](https://camo.githubusercontent.com/edda1494444cec7fd2cc001d99f617f8621ba48b14ab807c0e566f8d6f6f6d3b/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f626564746f6f6c73) |
|
https://bedtools.readthedocs.io/en/latest/ https://github.com/arq5x/bedtools2 |
berrywood-report-env ![docker pulls](https://camo.githubusercontent.com/e3a08846d93b7bb4f2ae32ffeeeb2f329266c301f2ad2a78616c7eaba2ed684c/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f6265727279776f6f642d7265706f72742d656e76) |
|
none |
blast+ ![docker pulls](https://camo.githubusercontent.com/77b6818f3199787fe2253a39e7293d274f1a110bed6200d0528977ce1ea9e8f1/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f626c617374) |
|
https://www.ncbi.nlm.nih.gov/books/NBK279690/ |
bowtie2 ![docker pulls](https://camo.githubusercontent.com/26fc180ade3a9789beadad9e7d16a5ccd9428a1a933e42086ac0f141e83c18bc/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f626f7774696532) |
|
http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml https://github.com/BenLangmead/bowtie2 |
BWA ![docker pulls](https://camo.githubusercontent.com/81162cf752399a72daf85d840b8b50e6cfa8cf83bcdc1b04675d018965f8ccee/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f627761) |
|
https://github.com/lh3/bwa |
Canu ![docker pulls](https://camo.githubusercontent.com/de0d9f079c6859b94c7c310a944ea446d1bc1192fd29de0c951e8526d1f75dbc/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f63616e753f) |
|
https://canu.readthedocs.io/en/latest/ https://github.com/marbl/canu |
Canu-Racon ![docker pulls](https://camo.githubusercontent.com/8e3193c228b0f13781aab3c6a5fd27c6d697f38053566097f421fffad9ae60ef/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f63616e752d7261636f6e) |
- 1.7.1 (Canu), 1.3.1 (Racon), 2.13 (minimap2)
- 1.9 (Canu), 1.4.3 (Racon), 2.17 (minimap2)
- 1.9i (Canu), 1.4.3 (Racon), 2.17 (minimap2), (+racon_preprocess.py)
- 2.0 (Canu), 1.4.3 (Racon), 2.17 (minimap2)
|
https://canu.readthedocs.io/en/latest/ https://github.com/lbcb-sci/racon https://github.com/isovic/racon (ARCHIVED) https://lh3.github.io/minimap2/ |
centroid ![docker pulls](https://camo.githubusercontent.com/5e976a74f3f4a638774f0afb72297ec9c398fbbc7c8cd38a6f302d3dd41ed699/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f63656e74726f6964) |
|
https://github.com/stjacqrm/centroid |
CDC-SPN ![docker pulls](https://camo.githubusercontent.com/cc07b30e81bead91afc09b0d1138480fd0ec6732aa395024e12ce37853f5815b/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f6364632d73706e) |
|
https://github.com/BenJamesMetcalf/Spn_Scripts_Reference |
cfsan-snp-pipeline ![docker pulls](https://camo.githubusercontent.com/a77a0a58eeff2e5ecdf57329bb551392d6e1739e1fbc4e364c6456079d848147/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f636673616e2d736e702d706970656c696e65) |
|
https://github.com/CFSAN-Biostatistics/snp-pipeline |
Circlator ![docker pulls](https://camo.githubusercontent.com/cc1cd0b00501984d7968a897da64031ea17029bd813916d5e6945e9d99550496/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f636972636c61746f72) |
|
https://github.com/sanger-pathogens/circlator |
Clustalo ![docker pulls](https://camo.githubusercontent.com/c466d4b9e51cdb764a61c7bf84d65ba52ef456e5d33c776be4278c6020862a13/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f636c757374616c6f) |
|
http://www.clustal.org/omega/ |
colorid ![docker pulls](https://camo.githubusercontent.com/496c6d530ef52f98244f3f219b7a09872af88ad968b7997374c5aa9c93d882b8/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f636f6c6f726964) |
|
https://github.com/hcdenbakker/colorid |
cutshaw-report-env ![docker pulls](https://camo.githubusercontent.com/4c022b61c2af6bf4416641af2cfcca092eaa19386a14823f3066205e583dad87/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f637574736861772d7265706f72742d656e76) |
|
https://github.com/VADGS/CutShaw |
datasets-sars-cov-2 ![docker pulls](https://camo.githubusercontent.com/06519971039c67fbbf9d9dc5a3d85c4e8a47e8b9baedeae9afbf24d33bce07ba/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f64617461736574732d736172732d636f762d32) |
|
https://github.com/CDCgov/datasets-sars-cov-2 |
dnaapler ![docker pulls](https://camo.githubusercontent.com/e49991a80681daef2905261455ff8799f471bca32b7ddd98fb77fec7de6b9c2a/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f646e6161706c6572) |
|
https://github.com/gbouras13/dnaapler |
dragonflye ![docker pulls](https://camo.githubusercontent.com/7a1b6d4e90f0accbf2fd8402bc6c50588f763c155e65bdd15060cfcc0b4ff9fb/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f647261676f6e666c7965) |
|
https://github.com/rpetit3/dragonflye |
DSK ![docker pulls](https://camo.githubusercontent.com/e152d466277b43a08cfce504ed14be2c162abee4abed5dc9eba6ad2c2631b09b/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f64736b) |
|
https://gatb.inria.fr/software/dsk/ |
emboss ![docker pulls](https://camo.githubusercontent.com/57179e33b183eb7603994d853a007e19e3a55977c92232de4a3f206a082ffe61/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f656d626f7373) |
|
http://emboss.sourceforge.net |
emmtyper ![docker pulls](https://camo.githubusercontent.com/6111577f868025fe8948a61674e0ca9404e69c4f0dcbde653be59796189274cd/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f656d6d7479706572) |
|
https://github.com/MDU-PHL/emmtyper |
emm-typing-tool ![docker pulls](https://camo.githubusercontent.com/4aee0fe4049d78badc3e268911e43a85d6b6363fb3d5273878ce2bc995e447d5/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f656d6d2d747970696e672d746f6f6c) |
|
https://github.com/phe-bioinformatics/emm-typing-tool |
EToKi ![docker pulls](https://camo.githubusercontent.com/702d1d4efa1f10a3b3f1f9d95de2228c12d4c7b4aa239c3794e71f10bb084f21/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f65746f6b69) |
|
https://github.com/zheminzhou/EToKi |
FastANI ![docker pulls](https://camo.githubusercontent.com/b63110c88ebeb320ed4aeee391552005f7bce1ebac8ea171f90f1d1b92a47d2e/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f66617374616e69) |
|
https://github.com/ParBLiSS/FastANI |
Fastp ![docker pulls](https://camo.githubusercontent.com/318ce1ca776aa8924b7864c393a69d149e82d1546dd44e9cd1ed44b81c80b9ad/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f6661737470) |
|
http://opengene.org/fastp/ https://github.com/OpenGene/fastp |
FastTree ![docker pulls](https://camo.githubusercontent.com/78f43f09d0e8fcc21faf1d3afeb8dfa7561e9248c8aca26543be14d9bd72460f/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f6661737474726565) |
|
http://www.microbesonline.org/fasttree/ |
FastQC ![docker pulls](https://camo.githubusercontent.com/bb9a4eb2acc495d5050e2415ee398f0b4f2d715c34354efaa15c23a3252e145a/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f666173747163) |
|
https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ https://github.com/s-andrews/FastQC |
fastq-scan ![docker pulls](https://camo.githubusercontent.com/40a856e1b8e1c4a4ccf4d6472792d30c4fef3c4bd149a86eb68b4d4293ea02e2/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f66617374712d7363616e) |
|
https://github.com/rpetit3/fastq-scan |
Freebayes ![docker pulls](https://camo.githubusercontent.com/b95e46f105fe79f34ef15c671f15cc73bfb0dcf827e1d19d12d8f1b1ce97f8bd/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f667265656261796573) |
|
https://github.com/freebayes/freebayes |
Filtlong ![docker pulls](https://camo.githubusercontent.com/f198a2a21cf12039d7d1ed5ba70f8946cdc007f7567bbe1659533b39e812f2e3/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f66696c746c6f6e67) |
|
https://github.com/rrwick/filtlong |
FLASH ![docker pulls](https://camo.githubusercontent.com/b630e18b82e0cbfe4f75387ee831f028f3202297aa30771dd0ff91ecf733393b/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f666c617368) |
|
http://ccb.jhu.edu/software/FLASH |
Flye ![docker pulls](https://camo.githubusercontent.com/8be4402d08213c6df902db2d0102424b31385c9792646a50560a409e2fd948a6/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f666c7965) |
|
https://github.com/fenderglass/Flye |
Freyja ![docker pulls](https://camo.githubusercontent.com/57cf338dca55c0286483fba88b1467de0ce82cbd64ffdea596bf5871af64934c/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f667265796a61) |
- 1.2
- 1.2.1
- 1.3.1
- 1.3.2
- 1.3.4
- 1.3.7
- 1.3.8
- 1.3.9
- 1.3.10
- 1.3.11
- 1.3.12
- 1.4.2
- 1.4.3
|
https://github.com/andersen-lab/Freyja |
GAMBIT ![docker pulls](https://camo.githubusercontent.com/c9d5c4bead2bd579a6d6d5fc7e54ff577448f2ae36d28499d0bcbbe4f754e2b5/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f67616d626974) |
|
https://github.com/jlumpe/gambit |
GAMMA ![docker pulls](https://camo.githubusercontent.com/085a94bcbb6e008f67437761f28f9d767a94320e5cbc69c06f3ef18a16e793e5/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f67616d6d61) |
|
https://github.com/rastanton/GAMMA/ |
gfastats ![docker pulls](https://camo.githubusercontent.com/0382c5e21a1fe78a507b2731bbb92592cc3931c6ee3f69387de63a60d8567dd2/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f6766617374617473) |
|
https://github.com/vgl-hub/gfastats |
hmmer ![docker pulls](https://camo.githubusercontent.com/34238520ee6cda87a48487a68e25edf58425b770ecabed650b3a58ec0030d280/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f686d6d6572) |
|
http://hmmer.org/ |
homopolish ![docker pulls](https://camo.githubusercontent.com/5651e2c8e0adbac5470397082e5507a555b74d166925be39641447789ea2633e/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f686f6d6f706f6c697368) |
|
https://github.com/ythuang0522/homopolish/ |
htslib ![docker pulls](https://camo.githubusercontent.com/3a418325f8f68f9818eacf98eac82fb9987a71eba599d709175b787aba2dbb63/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f6874736c6962) |
|
https://www.htslib.org/ |
iqtree ![docker pulls](https://camo.githubusercontent.com/ec7796601fe7597284fb6daffe686f66fd2139a46b3b83806c187fad3f763e79/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f697174726565) |
|
http://www.iqtree.org/ |
iqtree2 ![docker pulls](https://camo.githubusercontent.com/6d60eafb43392607c3879ef2fa4e4cbe55ba044c7473ae5009e961fc5dd1205a/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f69717472656532) |
|
http://www.iqtree.org/ |
IRMA ![docker pulls](https://camo.githubusercontent.com/b6237994692bdba56a9e7eeb01701a5eb8e7afa2ca8a90ef3f7eba16b0dd7c0b/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f69726d61) |
|
https://wonder.cdc.gov/amd/flu/irma/ |
iVar ![docker pulls](https://camo.githubusercontent.com/c6a73a3420b4985e84f4f95be96d24ae36ee18b0e60e3620e0606c844f59f8b3/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f69766172) |
- 1.1
- 1.1 (+SARS-CoV2 reference)
- 1.2.1
- 1.2.1 (+SC2 ref)
- 1.2.2 (+SC2 ref and artic bedfiles)
- 1.3
- 1.3.1
- 1.3.2
- 1.4.1
- 1.4.2
|
https://github.com/andersen-lab/ivar |
Kaptive ![docker pulls](https://camo.githubusercontent.com/6309058cfbbc99d2d27b5854b9fe075ebf41c553fa61f4bc06c453cd105f5101/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f6b617074697665) |
|
https://github.com/katholt/Kaptive/ |
Kleborate ![docker pulls](https://camo.githubusercontent.com/287f397bcb25ac83089c1d6d230aea4b4ca50623ba67d57b0c2b80afde6a7897/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f6b6c65626f72617465) |
|
https://github.com/katholt/Kleborate/ https://github.com/katholt/Kaptive/ |
kma ![docker pulls](https://camo.githubusercontent.com/c9bec2f08e4a8322a552d26cfc42d6ed3800a093967f191c4efbf80d85d1920c/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f6b6d61) |
- 1.2.21
- 1.4.10 (no database)
|
https://bitbucket.org/genomicepidemiology/kma/ |
Kraken ![docker pulls](https://camo.githubusercontent.com/05f30ff1322312c312db886b4d5947c325c82e91086827bcfb49fe889a972ea0/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f6b72616b656e) |
- 1.0
- 1.1.1
- 1.1.1 (no database)
|
https://github.com/DerrickWood/kraken |
Kraken2 ![docker pulls](https://camo.githubusercontent.com/709811965c5a70ff3c160ab3d9041e5041ebbfa03e71b62704f5bf40bfa0c4cd/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f6b72616b656e32) |
- 2.0.8-beta (no database)
- 2.0.8-beta (MiniKraken2_v1_8GB db)
- 2.0.8-beta_hv (human + virus db)
- 2.0.9-beta (no db)
- 2.0.9-beta (Minikraken v2 RefSeq: bacteria, archaea, viral, and human 8GB db)
- 2.1.0 (no db)
- 2.1.1 (no db)
- 2.1.2 (no db)
|
https://github.com/DerrickWood/kraken2 |
kSNP3 ![docker pulls](https://camo.githubusercontent.com/89902cdc69c3a54ec93331eb22fc981e41eaf538afe546903d2c56fd5955b9fe/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f6b736e7033) |
|
https://sourceforge.net/projects/ksnp/ |
kSNP4 ![docker pulls](https://camo.githubusercontent.com/905e32fce3749e9ae7449ce2f493c2784c0c9ba2c2f21c71b6ddb95033a56220/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f6b736e7034) |
|
https://sourceforge.net/projects/ksnp/ |
legsta ![docker pulls](https://camo.githubusercontent.com/23d3ab08592386a081f8a6557e34edbc3d2330dcbd6ea4c2643245fe7b62091c/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f6c6567737461) |
|
https://github.com/tseemann/legsta |
liftoff ![docker pulls](https://camo.githubusercontent.com/1bfbfbefede72769cbee2673c180858d920c055f1a1566c3e4169bcdb003c329/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f6c6966746f6666) |
|
https://github.com/agshumate/Liftoff |
Lyve-SET (includes CG-Pipeline scripts and raxml) ![docker pulls](https://camo.githubusercontent.com/3fb18ebaca6df77e9e030a68a025d039a7ca947617c3769961bf48a9ef98df3c/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f6c797665736574) |
|
https://github.com/lskatz/lyve-SET https://github.com/lskatz/CG-Pipeline |
MAFFT ![docker pulls](https://camo.githubusercontent.com/aeb0939041eb949e4129cca8ea914e9d9214acf0b1c28e7cf36378a3ab1317ab/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f6d61666674) |
|
https://mafft.cbrc.jp/alignment/software/ |
Mash ![docker pulls](https://camo.githubusercontent.com/0ae534160eed5f7dfeeaf68d46769700e1965f17d393099965dfe670fd57a563/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f6d617368) |
|
https://github.com/marbl/Mash |
mashtree ![docker pulls](https://camo.githubusercontent.com/ab673901bda13145ebd24f1608ef7bf18f9ad5aa5812cebfd69a3e80642d8eff/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f6d61736874726565) |
|
https://github.com/lskatz/mashtree |
MaSuRCA ![docker pulls](https://camo.githubusercontent.com/d073989c981b45edcf9d78f960f850591467120f3b40a120ad4e95ee5af9127a/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f6d617375726361) |
|
https://github.com/alekseyzimin/masurca |
medaka ![docker pulls](https://camo.githubusercontent.com/f1eea316494d281abc13a2c1c3ecbba4b20da6b83eec3f960e80583ef1aa4c56/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f6d6564616b61) |
|
https://github.com/nanoporetech/medaka |
metaphlan ![docker pulls](https://camo.githubusercontent.com/7fc9116fc49a953e88bcad9894ff8a40c81ae67171088060756ca0c55470eb1d/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f6d65746170686c616e) |
- 3.0.3-no-db (no database)
- 3.0.3 (~3GB db)
|
https://github.com/biobakery/MetaPhlAn/tree/3.0 |
minimap2 ![docker pulls](https://camo.githubusercontent.com/991f1813ba0755091d3c8fd680b72baab4928767ebadf46a3794b515ead76c81/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f6d696e696d617032) |
- 2.17
- 2.18
- 2.21
- 2.22
- 2.23
- 2.24
- 2.25
|
https://github.com/lh3/minimap2 |
minipolish ![docker pulls](https://camo.githubusercontent.com/3b4f58db470fed46b2803a6be287c9ae4b6cda1c52833ae6038ea3c761b34d6c/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f6d696e69706f6c697368) |
|
https://github.com/rrwick/Minipolish |
mlst ![docker pulls](https://camo.githubusercontent.com/f30073899ec4ca5f62dbe1b1987613b365d7483ead89ca9f18fb7cd68b4aecdc/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f6d6c7374) |
- 2.16.2
- 2.17.6
- 2.19.0
- 2.22.0
- 2.22.1
- 2.23.0
|
https://github.com/tseemann/mlst |
Mugsy ![docker pulls](https://camo.githubusercontent.com/808d5ca407a5850028973bcf5bfc3c25af43af51efbff4c74684f829fa851611/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f6d75677379) |
|
http://mugsy.sourceforge.net/ |
MultiQC ![docker pulls](https://camo.githubusercontent.com/ba595687c31d093d5ae5a7aa2e4f6d5def26abdef5a2e640e1a8c5ff5ab387e9/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f6d756c74697163) |
|
https://github.com/ewels/MultiQC |
Mummer ![docker pulls](https://camo.githubusercontent.com/76c18de621d7f20e4ef195af48e11ef052c7dedeb3b4e6242dfc38de472887c6/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f6d756d6d6572) |
- 4.0.0
- 4.0.0 + RGDv2
- 4.0.0 + RGDv2 + gnuplot
|
https://github.com/mummer4/mummer |
Mykrobe + Genotyphi + sonneityping ![docker pulls](https://camo.githubusercontent.com/bc0baac80b22e8b225bf58a95c48ad94a7e10bfa6ff72af62e675f9b5037c6b1/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f6d796b726f6265) |
- 0.11.0 (Mykrobe) & 1.9.1 (Genotyphi)
- 0.12.1 (Mykrobe) & 1.9.1 (Genotyphi) & v20210201 (sonneityping)
- 0.12.1 (Mykrobe) & 2.0 (Genotyphi) & v20210201 (sonneityping)
|
https://github.com/Mykrobe-tools/mykrobe https://github.com/typhoidgenomics/genotyphi https://github.com/katholt/sonneityping |
NanoPlot ![docker pulls](https://camo.githubusercontent.com/896441378d28ab25c02de9c434703acd33f5fc5acdf59e44de03e8544ed970c5/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f6e616e6f706c6f74) |
- 1.27.0
- 1.29.0
- 1.30.1
- 1.32.0
- 1.33.0
- 1.40.0
|
https://github.com/wdecoster/NanoPlot |
ngmaster ![docker pulls](https://camo.githubusercontent.com/cfd95cae66482af8ab3571ef2c17a3a57654e23e4b15ae11d31791da33a1ed65/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f6e676d6173746572) |
|
https://github.com/MDU-PHL/ngmaster |
NCBI Datasets ![docker pulls](https://camo.githubusercontent.com/63810a47ec3c49061fc48a03eafd244968e3344162fa91722c47fa7ce08d30c5/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f6e6362692d6461746173657473) |
Click to see all datasets versions datasets versions |
https://github.com/ncbi/datasets https://www.ncbi.nlm.nih.gov/datasets/docs/v1/ |
NCBI AMRFinderPlus ![docker pulls](https://camo.githubusercontent.com/e2c307616c57a85e3e8681f1e12591c2c4d71ad592383a470d7cac73081657f2/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f6e6362692d616d7266696e646572706c7573) |
AMRFinderPlus & database verion Click to see AMRFinderplus v3.11.4 and older versions! - 3.1.1b
- 3.8.4
- 3.8.28
- 3.9.3
- 3.9.8
- 3.10.1
- 3.10.5
- 3.10.16
- 3.10.20
- 3.10.24
- 3.10.30
- 3.10.36
- 3.10.42
- 3.11.2 & 2022-12-19.1
- 3.11.2 & 2023-02-23.1
- 3.11.4 & 2023-02-23.1
- 3.11.8 & 2023-02-23.1
- 3.11.11 & 2023-04-17.1
|
https://github.com/ncbi/amr |
NCBI table2asn ![docker pulls](https://camo.githubusercontent.com/0019bbdac6f7ed1115ffe50ba2a125593013b19938620c9088c735500afc2fc4/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f6e6362692d7461626c653261736e) |
|
https://www.ncbi.nlm.nih.gov/genbank/table2asn/ https://ftp.ncbi.nlm.nih.gov/asn1-converters/versions/2022-06-14/by_program/table2asn/ |
OrthoFinder ![docker pulls](https://camo.githubusercontent.com/f4e825f03dfe461aa81e0dcfc70751892123efa0b85eb8d2d5d77fa90acb461a/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f6f7274686f66696e646572) |
|
https://github.com/davidemms/OrthoFinder |
Panaroo ![docker pulls](https://camo.githubusercontent.com/7778ee607143151c1d5bcde54c710dfd66904fdfa8dc9bf554b8993c09adc90e/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f70616e61726f6f) |
|
https://github.com/gtonkinhill/panaroo |
Pangolin ![docker pulls](https://camo.githubusercontent.com/a9ddd8d8aa94d2b0a152c4475f6848c7d0f6e86540345908131e007ef40b9613/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f70616e676f6c696e) |
Click to see Pangolin v3 and older versions! Pangolin version & pangoLEARN data release date - 1.1.14
- 2.0.4 & 2020-07-20
- 2.0.5 & 2020-07-20
- 2.1.1 & 2020-12-17
- 2.1.3 & 2020-12-17
- 2.1.6 & 2021-01-06
- 2.1.7 & 2021-01-11
- 2.1.7 & 2021-01-20
- 2.1.8 & 2021-01-22
- 2.1.10 & 2021-02-01
- 2.1.11 & 2021-02-01
- 2.1.11 & 2021-02-05
- 2.2.1 & 2021-02-06
- 2.2.2 & 2021-02-06
- 2.2.2 & 2021-02-11
- 2.2.2 & 2021-02-12
- 2.3.0 & 2021-02-12
- 2.3.0 & 2021-02-18
- 2.3.0 & 2021-02-21
- 2.3.2 & 2021-02-21
- 2.3.3 & 2021-03-16
- 2.3.4 & 2021-03-16
- 2.3.5 & 2021-03-16
- 2.3.6 & 2021-03-16
- 2.3.6 & 2021-03-29
- 2.3.8 & 2021-04-01
- 2.3.8 & 2021-04-14
- 2.3.8 & 2021-04-21
- 2.3.8 & 2021-04-23
- 2.4 & 2021-04-28
- 2.4.1 & 2021-04-28
- 2.4.2 & 2021-04-28
- 2.4.2 & 2021-05-10
- 2.4.2 & 2021-05-11
- 2.4.2 & 2021-05-19
- 3.0.5 & 2021-06-05
- 3.1.3 & 2021-06-15
- 3.1.5 & 2021-06-15
- 3.1.5 & 2021-07-07-2
- 3.1.7 & 2021-07-09
- 3.1.8 & 2021-07-28
- 3.1.10 & 2021-07-28
- 3.1.11 & 2021-08-09
- 3.1.11 & 2021-08-24
- 3.1.11 & 2021-09-17
- 3.1.14 & 2021-09-28
- 3.1.14 & 2021-10-13
- 3.1.16 & 2021-10-18
- 3.1.16 & 2021-11-04
- 3.1.16 & 2021-11-09
- 3.1.16 & 2021-11-18
- 3.1.16 & 2021-11-25
- 3.1.17 & 2021-11-25
- 3.1.17 & 2021-12-06
- 3.1.17 & 2022-01-05
- 3.1.18 & 2022-01-20
- 3.1.19 & 2022-01-20
- 3.1.20 & 2022-02-02
- 3.1.20 & 2022-02-28
Pangolin version & pangolin-data version
- 4.0 & 1.2.133
- 4.0.1 & 1.2.133
- 4.0.2 & 1.2.133
- 4.0.3 & 1.2.133
- 4.0.4 & 1.2.133
- 4.0.5 & 1.3
- 4.0.6 & 1.6
- 4.0.6 & 1.8
- 4.0.6 & 1.9
- 4.1.1 & 1.11
- 4.1.2 & 1.12
- 4.1.2 & 1.13
- 4.1.2 & 1.14
- 4.1.3 & 1.15.1
- 4.1.3 & 1.16
- 4.1.3 & 1.17
- 4.2 & 1.18
- 4.2 & 1.18.1
- 4.2 & 1.18.1.1
- 4.2 & 1.19
- 4.3 & 1.20
|
https://github.com/cov-lineages/pangolin https://github.com/cov-lineages/pangoLEARN https://github.com/cov-lineages/pango-designation https://github.com/cov-lineages/scorpio https://github.com/cov-lineages/constellations https://github.com/cov-lineages/lineages (archived) https://github.com/hCoV-2019/pangolin (archived) |
parallel-perl ![docker pulls](https://camo.githubusercontent.com/0a6a5093f2ca0b8edfe93fd1806598ff73689a3df2eb16cb52b200313ec77d27/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f706172616c6c656c2d7065726c) |
|
https://www.gnu.org/software/parallel |
pasty ![docker pulls](https://camo.githubusercontent.com/a74a7d122b74ceb2a2aa3ee1796ef5295459992bcc4919192af366bc47ba139c/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f7061737479) |
|
https://github.com/rpetit3/pasty |
pbptyper ![docker pulls](https://camo.githubusercontent.com/b09c7f6cfde15ea0f5d072ca81442d42f3533221d0befb548839fdb352a69839/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f7062707479706572) |
|
https://github.com/rpetit3/pbptyper |
Phyml ![docker pulls](https://camo.githubusercontent.com/27f497be7a664f55c2bbe35d94a25d84f12d9261f103eac936a9a90354cb540d/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f7068796d6c) |
|
https://github.com/stephaneguindon/phyml |
Piggy ![docker pulls](https://camo.githubusercontent.com/d18a5e8704c16e78bba2ce9fd2087d93d4c08a18caa4f68b74d77ed6c609b4e7/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f7069676779) |
|
https://github.com/harry-thorpe/piggy |
Pilon ![docker pulls](https://camo.githubusercontent.com/abc04508daaa9f4e1611b7769ca9ee97dee7f7670e7657f668463d3d2a7fbdb1/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f70696c6f6e) |
|
https://github.com/broadinstitute/pilon |
Piranha ![docker pulls](https://camo.githubusercontent.com/82b42f7df8619766a97f2672b4652a08061da326bc68284014178a6fe6b2c711/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f706972616e6861) |
|
https://github.com/polio-nanopore/piranha |
PlasmidFinder ![docker pulls](https://camo.githubusercontent.com/c5d10a42def186ae7bd792385e6792bf074fc847e0385cfeef9286a5a18d8904/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f706c61736d696466696e646572) |
|
https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/ |
PlasmidSeeker ![docker pulls](https://camo.githubusercontent.com/e53ecfba7fbd81b823ee2a76387b3efa72806a287b2fdbe62fb912069b378c11/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f706c61736d69647365656b6572) |
|
https://github.com/bioinfo-ut/PlasmidSeeker |
pmga ![docker pulls](https://camo.githubusercontent.com/3e3c6ad1fb780fba97ac66c281d344c739b72c0aef2944c382c0a063e98910d1/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f706d6761) |
|
https://github.com/rpetit3/pmga |
polypolish ![docker pulls](https://camo.githubusercontent.com/d9928d99bfed0d7403868ed15b53a02d81efde12abbc010d8dd29c7b8cdc2010/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f706f6c79706f6c697368) |
|
https://github.com/rrwick/Polypolish |
PopPUNK ![docker pulls](https://camo.githubusercontent.com/b3268ae69f582c23ea79426d9f3ae2f9c50c27da0f825488727d2fee9a78b32b/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f706f7070756e6b) |
|
https://github.com/bacpop/PopPUNK |
Porechop ![docker pulls](https://camo.githubusercontent.com/61570a11767775fa02b48f57a4bd9c721e8e50a4f6aa579dc6bdc9d6dd2ee163/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f706f726563686f70) |
|
https://github.com/rrwick/Porechop |
Prokka ![docker pulls](https://camo.githubusercontent.com/3eff255d549d98fd0663b5dea438866f39d3aa92c2b42f19adcf0c5b699c31e0/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f70726f6b6b61) |
|
https://github.com/tseemann/prokka |
pyGenomeViz ![docker pulls](https://camo.githubusercontent.com/71cce79b9253fc038b14fdb3d57282961642f29f7be2aa5c93d7501c9166dfac/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f707967656e6f6d6576697a) |
|
https://github.com/moshi4/pyGenomeViz |
QUAST ![docker pulls](https://camo.githubusercontent.com/ac72c86ce7e8b9fe423baef58c7323154c419237f1edd4e488d8f49bf0e7b474/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f7175617374) |
|
https://github.com/ablab/quast |
QuickSNP ![docker pulls](https://camo.githubusercontent.com/ca347beb8517e72ffef48ad789b5d388b5a21db938828b5fead9c5076dfe47d3/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f717569636b736e70) |
|
https://github.com/k-florek/QuickSNP |
racon ![docker pulls](https://camo.githubusercontent.com/a9c1dfc6032b80ea39477e43b9a8ca69e08148e333d5d916c5dc853f5f820ead/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f7261636f6e) |
|
https://github.com/lbcb-sci/racon https://github.com/isovic/racon (ARCHIVED) |
rasusa ![docker pulls](https://camo.githubusercontent.com/c1d8a4ea8775de21ce916166362cff63b642e48a69ce72bed7c897a0c62c2ee4/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f726173757361) |
- 0.1.0
- 0.2.0
- 0.3.0
- 0.6.0
- 0.7.0
|
https://github.com/mbhall88/rasusa |
raven ![docker pulls](https://camo.githubusercontent.com/82d456da80993182c409332c550ed2a2f0e2e3268afb61002a4e96def1d24a07/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f726176656e) |
|
https://github.com/lbcb-sci/raven |
RAxML ![docker pulls](https://camo.githubusercontent.com/77d7cd3b7cb94657268a2e7b39b3ab87a5f0a1d80f50e8b81594f1d082363857/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f7261786d6c) |
- 8.2.12 (RAxML) and 0.9.0 (RAxML Next Generation)
|
https://github.com/stamatak/standard-RAxML https://github.com/amkozlov/raxml-ng |
ResFinder ![docker pulls](https://camo.githubusercontent.com/75e40fea536f23326e54b02de80c4ae0c51ed737dda9bab4542ce290c500c63e/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f72657366696e646572) |
|
https://bitbucket.org/genomicepidemiology/resfinder/src/master/ |
Roary ![docker pulls](https://camo.githubusercontent.com/3750a4b9e1f06ad121950fac7b918abfe10c54a31e6190856e34f38d801d182c/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f726f617279) |
|
https://github.com/sanger-pathogens/Roary |
SalmID ![docker pulls](https://camo.githubusercontent.com/e7982457844b6e2923529f32865109f0d79dabd97b8eb5dd2c06a1907efb7276/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f73616c6d6964) |
|
https://github.com/hcdenbakker/SalmID |
Samtools ![docker pulls](https://camo.githubusercontent.com/9b78a3ef151a9e976744e196b54bec78c661cf77da2f145e85bd668801a44d4a/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f73616d746f6f6c73) |
|
https://github.com/samtools/samtools |
SeqKit ![docker pulls](https://camo.githubusercontent.com/3057a297804052f64ecc52cec542f11924283e39e12e150097463058dcaa3ec6/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f7365716b6974) |
|
https://github.com/shenwei356/seqkit |
SeqSero ![docker pulls](https://camo.githubusercontent.com/e2e4948e001a8862bee939d1e33c4991a947a36c3996caabff5395801c519f46/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f7365717365726f) |
|
https://github.com/denglab/SeqSero |
SeqSero2 ![docker pulls](https://camo.githubusercontent.com/d3ac10b2a707c0b287fa3d41f6bcd1dfe3c6fe403ddc2ca8ffc15d95fe0732b9/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f7365717365726f32) |
- 0.1.0
- 1.0.0
- 1.0.2
- 1.1.0
- 1.1.1
- 1.2.1
|
https://github.com/denglab/SeqSero2/ |
seqtk ![docker pulls](https://camo.githubusercontent.com/9095a5bc3cdfa2e0d6591206ea2fb0948527e7df69fc68f09bb3982c05893b03/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f736571746b) |
|
https://github.com/lh3/seqtk |
seqyclean ![docker pulls](https://camo.githubusercontent.com/87e8950a7da2d0ee8e7c3c7c3c41cf131ea23157b4883a268122b43a75380a48/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f73657179636c65616e) |
|
https://github.com/ibest/seqyclean |
Seroba ![docker pulls](https://camo.githubusercontent.com/c38c91e27e97911aa4811bdfd6adcd4ca3d3d6eeb8f93b868db831b5be1c80db/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f7365726f6261) |
|
https://github.com/sanger-pathogens/seroba |
SerotypeFinder ![docker pulls](https://camo.githubusercontent.com/ffefeff4aedb219e9dcbbc02ddff1791e05c041691150ecbbb7c5d3ebe97e41c/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f7365726f7479706566696e646572) |
- 1.1 (perl version)
- 2.0.1 (python version)
|
https://bitbucket.org/genomicepidemiology/serotypefinder/ |
shigatyper ![docker pulls](https://camo.githubusercontent.com/872b4a30e1f5acf0407e7ab8b37255b1578b9347e2c202c422b423e718f52e98/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f73686967617479706572) |
|
https://github.com/CFSAN-Biostatistics/shigatyper |
ShigEiFinder ![docker pulls](https://camo.githubusercontent.com/d07972f67dd31d953761d9cb2320ddca4a6e359217f5523cfeb7f23f4c77ec4e/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f73686967656966696e646572) |
|
https://github.com/LanLab/ShigEiFinder |
Shovill ![docker pulls](https://camo.githubusercontent.com/1a69a9925ed8daf9a25ed22eb978e9df516c4cc1e33b9ce6307bd8c6cedc23f2/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f73686f76696c6c) |
|
https://github.com/tseemann/shovill |
Shovill-se ![docker pulls](https://camo.githubusercontent.com/88c719aab2e004c83298fb30ca88f941480b2443df150f38b288a8edf7fb5200/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f73686f76696c6c2d7365) |
|
https://github.com/rpetit3/shovill/tree/v1.1.0se |
SISTR ![docker pulls](https://camo.githubusercontent.com/a45dd9d9cf5374b8983d394a034edab35dfec26f5acac7f27a361e320f896cc5/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f7369737472) |
|
https://github.com/phac-nml/sistr_cmd |
SKA ![docker pulls](https://camo.githubusercontent.com/8e5e402a4dba1bf93cf4581bd61faee9121b4fdf9baca680b2ca54c3104da2a3/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f736b61) |
|
https://github.com/simonrharris/SKA |
SKESA ![docker pulls](https://camo.githubusercontent.com/01e36f351cd1c4cf3bec28e7549ae15a1f2413d480dc8a7b8e1f27b81f1b66cb/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f736b657361) |
- 2.3.0
- 2.4.0 (
gfa_connector & kmercounter included)
|
https://github.com/ncbi/SKESA |
Smalt ![docker pulls](https://camo.githubusercontent.com/f3876d9424b516a4b9d4ad22ae73e26bbbdbe1f25ae069af996b56ef1330992a/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f736d616c74) |
|
https://www.sanger.ac.uk/tool/smalt-0/ |
snpeff ![docker pulls](https://camo.githubusercontent.com/f369b03348f3575c37da11fd2fc85063de37c3fba73f2f91b86989318bba5b8d/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f736e70656666) |
|
https://pcingola.github.io/SnpEff |
Snippy ![docker pulls](https://camo.githubusercontent.com/3a24fb675615fcac12c03d867387c11221eae051129322e042bc1b53ec5c3bfb/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f736e69707079) |
|
https://github.com/tseemann/snippy |
snp-dists ![docker pulls](https://camo.githubusercontent.com/17d2bf46ffb2b03fd560b05961bbe02eb0fffb32d29463e430d409c42eaa968a/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f736e702d6469737473) |
|
https://github.com/tseemann/snp-dists |
SNP-sites ![docker pulls](https://camo.githubusercontent.com/cf6db9d07a377dc10a20384a0253c5787ff99a510e0bfacbddcedc899b25217a/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f736e702d7369746573) |
|
https://github.com/sanger-pathogens/snp-sites |
SNVPhyl-tools ![docker pulls](https://camo.githubusercontent.com/b007ffc03148e6fe2cf35c435f16059b985f7566c8151516f2905bd8fdee5bd5/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f736e767068796c2d746f6f6c73) |
|
https://github.com/phac-nml/snvphyl-tools |
SPAdes ![docker pulls](https://camo.githubusercontent.com/72f782bda35a5332ac0c6560b2ecf2b20e03d572dfbf9e88da302c9e4302b951/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f737061646573) |
- 3.8.2
- 3.12.0
- 3.13.0
- 3.14.0
- 3.14.1
- 3.15.0
- 3.15.1
- 3.15.2
- 3.15.3
- 3.15.4
- 3.15.5
|
https://github.com/ablab/spades http://cab.spbu.ru/software/spades/ |
SRA-toolkit ![docker pulls](https://camo.githubusercontent.com/633dfda5dbb716748e1d1a3276aa73059ee6e365906c539163b50415860044d5/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f737261746f6f6c6b6974) |
|
https://github.com/ncbi/sra-tools |
SRST2 ![docker pulls](https://camo.githubusercontent.com/b736d2a2c1c019366bf66797cb901ef8b520f0b7ec4ec81d3f46b460ba342a0e/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f7372737432) |
|
https://github.com/katholt/srst2 |
Staramr ![docker pulls](https://camo.githubusercontent.com/7e00fb4f3255693c6b2fdb490aa53445b35955dbae9c382c50674b629dc2d9bc/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f73746172616d72) |
|
https://github.com/phac-nml/staramr |
TBProfiler ![docker pulls](https://camo.githubusercontent.com/fcc62857c0c05dc4367e27f0cdbeb99b28ec31f8de7da93131946dee94cec2cc/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f746270726f66696c6572) |
|
https://github.com/jodyphelan/TBProfiler |
TipToft ![docker pulls](https://camo.githubusercontent.com/4ad52d606d56f56785965323d4643eada5cff3bcc59bacd965e33860a5fea296/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f746970746f6674) |
|
https://github.com/andrewjpage/tiptoft |
Tostadas ![docker pulls](https://camo.githubusercontent.com/154f2ea9a8e183382717277d53d5182b8068988f3a087303cc70b59473dba0f2/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f746f737461646173) |
|
https://github.com/CDCgov/tostadas |
Treemmer ![docker pulls](https://camo.githubusercontent.com/2bc70c4ba1e28087a2e714973c8ef842361f2ebeff53db697783a382a6200b6c/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f747265656d6d6572) |
|
https://git.scicore.unibas.ch/TBRU/Treemmer (archived, moved to GitHub) https://github.com/fmenardo/Treemmer |
Trimmomatic ![docker pulls](https://camo.githubusercontent.com/c056f88ad4428f3e1ed8a9cfb7e621159ab61123c9b0c94a46eb3102f3dee44d/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f7472696d6d6f6d61746963) |
|
http://www.usadellab.org/cms/?page=trimmomatic https://github.com/usadellab/Trimmomatic |
Trycycler ![docker pulls](https://camo.githubusercontent.com/c2d73091b21e1545b46c40a2e04c601f756fc5723f0d0dfb36e8fc9d27aa6bd7/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f7472796379636c6572) |
- 0.3.1
- 0.3.2
- 0.3.3
- 0.5.0
- 0.5.3
- 0.5.4
|
https://github.com/rrwick/Trycycler |
Unicycler ![docker pulls](https://camo.githubusercontent.com/7161c5ccc6391132ec2440655fd259ebd8644a65a381beabb0b1d3aa40eaffef/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f756e696379636c6572) |
|
https://github.com/rrwick/Unicycler |
VADR ![docker pulls](https://camo.githubusercontent.com/2428f8a727a61bfb412db77be97c6eb9ecf6c66e23e30b66438bc3286c1a47a2/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f76616472) |
- 1.1
- 1.1.2
- 1.1.3
- 1.2
- 1.2.1
- 1.3 & SARS-CoV-2 models 1.3-1
- 1.3 & SARS-CoV-2 models 1.3-2
- 1.4 & SARS-CoV-2 models 1.3-2
- 1.4.1 & SARS-CoV-2 models 1.3-2
- 1.4.2 & SARS-CoV-2 models 1.3-2, MPXV models 1.4.2-1
- 1.5 & SARS-CoV-2 models 1.3-2, MPXV models 1.4.2-1
- 1.5.1 & SARS-CoV-2 models 1.3-2, MPXV models 1.4.2-1, RSV models 1.5-2
|
https://github.com/nawrockie/vadr (archived, now redirects to ncbi/vadr) https://github.com/ncbi/vadr |
VIBRANT ![docker pulls](https://camo.githubusercontent.com/1822c328c64dca914d06a7ee540e07385ac6198dd633025e58064dec0a021b88/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f76696272616e74) |
|
https://github.com/AnantharamanLab/VIBRANT |
VIGOR4 ![docker pulls](https://camo.githubusercontent.com/63409570db2b2fd05574ba517efd25619ef2727352a700b8f4d15775e8e90a05/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f7669676f7234) |
|
https://github.com/JCVenterInstitute/VIGOR4 |
VirSorter2 ![docker pulls](https://camo.githubusercontent.com/087ac4a00920afd0e8a82fa7aa4be657934ae3401236a065074480bed95fb79a/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f766972736f7274657232) |
|
https://github.com/jiarong/VirSorter2 |
VirulenceFinder ![docker pulls](https://camo.githubusercontent.com/2f66e2421e18968050990f61a67f149a2b2185f66fa5f57456c87677b42ec68f/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f766972756c656e636566696e646572) |
|
https://bitbucket.org/genomicepidemiology/virulencefinder/src/master/ https://bitbucket.org/genomicepidemiology/virulencefinder_db/src/master/ |
wtdbg2 ![docker pulls](https://camo.githubusercontent.com/9737669d066e6727caa8a3c7da4c775fe5ff2a638a219305345ddfb7f0401c1d/68747470733a2f2f62616467656e2e6e65742f646f636b65722f70756c6c732f7374617068622f777464626732) |
|
https://github.com/ruanjue/wtdbg2 |