ABRicate ![docker pulls](https://camo.githubusercontent.com/1d269446933bfe0f400f19c0807dbc1acde4cd55ecb6937d5d8359aa059c8b79/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f61627269636174652e7376673f7374796c653d706f706f7574) |
0.8.7, 0.8.13, 0.8.13s (+serotypefinder db), 0.9.8, 1.0.0 |
https://github.com/tseemann/abricate |
ARIBA ![docker pulls](https://camo.githubusercontent.com/8c005f6563323fe6546a92276d063df81cdb6d04ed23aa558af61c169dc32b7b/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f61726962612e7376673f7374796c653d706f706f7574) |
2.14.4 |
https://github.com/sanger-pathogens/ariba |
Augur ![docker pulls](https://camo.githubusercontent.com/92c5b802253a27bf802a98824bc4b23f71c816193326493679963c316e17cf85/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f61756775722e7376673f7374796c653d706f706f7574) |
6.3.0, 7.0.2, 8.0.0, 9.0.0 |
https://github.com/nextstrain/augur |
Auspice ![docker pulls](https://camo.githubusercontent.com/b958fe8e60a026383f501d1d7a4ca0781263f9f0a3cb505639265913a2bfdca5/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f617573706963652e7376673f7374796c653d706f706f7574) |
2.12.0 |
https://github.com/nextstrain/auspice |
BBTools ![docker pulls](https://camo.githubusercontent.com/ce6444ab89d069576e20130427d1a4301acbd0d984eb857c28a6dc5d91de377d/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f6262746f6f6c732e7376673f7374796c653d706f706f7574) |
38.76, 38.86 |
https://jgi.doe.gov/data-and-tools/bbtools/ |
bcftools ![docker pulls](https://camo.githubusercontent.com/22dc8c4e15df1badaf0495475c3d8c12ec80f2a75cc93eb15e472ced8767dcc1/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f626366746f6f6c732e7376673f7374796c653d706f706f7574) |
1.10.2, 1.11 |
https://github.com/samtools/bcftools |
bedtools ![docker pulls](https://camo.githubusercontent.com/23933dec57bfb04739fa807437235021d7e4e873f36a69bb363142967ee9e7b9/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f626564746f6f6c732e7376673f7374796c653d706f706f7574) |
2.29.2 |
https://bedtools.readthedocs.io/en/latest/ |
BWA ![docker pulls](https://camo.githubusercontent.com/3b9c192629f9ca4d6ad790c7468883f3683241f7aae81e140a4c18b3ab31b581/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f6277612e7376673f7374796c653d706f706f7574) |
0.7.17 |
https://github.com/lh3/bwa |
Canu ![docker pulls](https://camo.githubusercontent.com/3cc14cf4c1dad6fb04251d1cbbd7433bf666b803713d73d55affcd82b6379538/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f63616e752e7376673f7374796c653d706f706f7574) |
2.0 |
https://canu.readthedocs.io/en/latest/ https://github.com/marbl/canu |
Canu-Racon ![docker pulls](https://camo.githubusercontent.com/f1df6735e9749415c885b1bb258575b0fcc450fbcf6c7f9ade07b4400f91ef3f/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f63616e752d7261636f6e2e7376673f7374796c653d706f706f7574) |
2.0 (Canu) 1.4.3 (Racon) 2.17 (minimap2); 1.9 (Canu) 1.4.3 (Racon) 2.17 (minimap2); 1.9i (Canu) 1.4.3 (Racon) 2.17 (minimap2) (+racon_preprocess.py); 1.7.1 (Canu) 1.3.1 (Racon) 2.13 (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/752dcef72e32692035ba969cb2ab1e7c809ac9573b95d31fb9ecc4ef6899f79d/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f63656e74726f69642e7376673f7374796c653d706f706f7574) |
1.0.0 |
https://github.com/stjacqrm/centroid |
CDC-SPN ![docker pulls](https://camo.githubusercontent.com/4470355aded2c83e05b5b9d030c93e84d5988c1c171d90b89a4bbf639146e193/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f6364632d73706e2e7376673f7374796c653d706f706f7574) |
0.1 (no version) |
https://github.com/BenJamesMetcalf/Spn_Scripts_Reference |
cfsan-snp-pipeline ![docker pulls](https://camo.githubusercontent.com/dec7b27f03418f4cbf49cd3a310e39f3bb2796aeb57362d3147a9110fa0dd978/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f636673616e2d736e702d706970656c696e652e7376673f7374796c653d706f706f7574) |
2.0.2 |
https://github.com/CFSAN-Biostatistics/snp-pipeline |
Circlator ![docker pulls](https://camo.githubusercontent.com/c58c413528c50522196c6e4d63d81e0f207e632b2e5155aea51005d203890f79/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f636972636c61746f722e7376673f7374796c653d706f706f7574) |
1.5.6 |
https://github.com/sanger-pathogens/circlator |
Clustalo ![docker pulls](https://camo.githubusercontent.com/dcf639919c615198ee2592bd5ac4550fdeb7f769eb7db7c5ffa85f9d47bc5c42/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f636c757374616c6f2e7376673f7374796c653d706f706f7574) |
1.2.4 |
http://www.clustal.org/omega/ |
cutshaw-report-env ![docker pulls](https://camo.githubusercontent.com/99fb52236c6978eb2a0cb888bb58efd4d79e39cc763e8504c5d4be0bfeb154f9/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f637574736861772d7265706f72742d656e762e7376673f7374796c653d706f706f7574) |
1.0.0 |
https://github.com/VADGS/CutShaw |
emm-typing-tool ![docker pulls](https://camo.githubusercontent.com/815be8abca38425dc1ee9ab669474511ea2e204db9dd1ca45484638c381d49e0/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f656d6d2d747970696e672d746f6f6c2e7376673f7374796c653d706f706f7574) |
0.0.1 (no version) |
https://github.com/phe-bioinformatics/emm-typing-tool |
FastANI ![docker pulls](https://camo.githubusercontent.com/551de95d9bec4620bffa7c3709bd9b14be053b5ded54695e412ecb5dc05b0e74/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f66617374616e692e7376673f7374796c653d706f706f7574) |
1.1 |
https://github.com/ParBLiSS/FastANI |
FastTree ![docker pulls](https://camo.githubusercontent.com/6e88ffda0bc21ff86b4acb9f88c45ef6c75e7a1250c6075a1179b6f9a438dd8d/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f66617374747265652e7376673f7374796c653d706f706f7574) |
2.1.11 |
http://www.microbesonline.org/fasttree/ |
FastQC ![docker pulls](https://camo.githubusercontent.com/475d48e1a3c98c33d01ce7f8d70ace50e1a2926dab6f0c650b2f1ff69d977a22/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f6661737471632e7376673f7374796c653d706f706f7574) |
0.11.8 |
https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ https://github.com/s-andrews/FastQC |
Filtlong ![docker pulls](https://camo.githubusercontent.com/83695d85a532e0a403d04955f0cc23874afc5dcd0a695b07a54a488507bf05e8/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f66696c746c6f6e672e7376673f7374796c653d706f706f7574) |
0.2.0 |
https://github.com/rrwick/filtlong |
Flye ![docker pulls](https://camo.githubusercontent.com/7804ccd391a6d0e9a47f42fc9b3922199812ba1070678138e822506e5d7d459e/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f666c79652e7376673f7374796c653d706f706f7574) |
2.5, 2.7, 2.8 |
https://github.com/fenderglass/Flye |
iqtree ![docker pulls](https://camo.githubusercontent.com/95fd5a74a0c5fef5cf2aad522ac9c89ae4d6b6590c386a72969dde76d064d1b4/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f6971747265652e7376673f7374796c653d706f706f7574) |
1.6.7 |
http://www.iqtree.org/ |
iVar ![docker pulls](https://camo.githubusercontent.com/32a27997f3d3469eded8930521b473a06c7a35ad24d1c3d76e07ae2247fd308a/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f697661722e7376673f7374796c653d706f706f7574) |
1.1, 1.1 (+ SARS-CoV2 reference), 1.2.1, 1.2.1 (+ SC2 ref), 1.2.2 (+SC2 ref and artic bedfiles) |
https://github.com/andersen-lab/ivar |
kma ![docker pulls](https://camo.githubusercontent.com/5ea116cf027f5727373b4b18efb7c713f1f52554c139a82375b1993fa782a9d5/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f6b6d612e7376673f7374796c653d706f706f7574) |
1.2.21 |
https://bitbucket.org/genomicepidemiology/kma/ |
Kraken ![docker pulls](https://camo.githubusercontent.com/51310d9782e496b700c5a67fc08b7b6a02a6d817ea88c3ab66b2d4bdf7fdcf0b/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f6b72616b656e2e7376673f7374796c653d706f706f7574) |
1.0, 1.1.1, 1.1.1 (no database) |
https://github.com/DerrickWood/kraken |
Kraken2 ![docker pulls](https://camo.githubusercontent.com/3d96b4ceb119aa1d004c7d7aa164ad251139f227f37056780dbf35982aab3247/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f6b72616b656e322e7376673f7374796c653d706f706f7574) |
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) |
https://github.com/DerrickWood/kraken2 |
kSNP3 ![docker pulls](https://camo.githubusercontent.com/58f5207bb1b18662cd348a0f7910d9d007c4425e64b8141708083e978592dcd5/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f6b736e70332e7376673f7374796c653d706f706f7574) |
3.1 |
https://sourceforge.net/projects/ksnp/ |
legsta ![docker pulls](https://camo.githubusercontent.com/120f9494e509c274d072a09b48a04bdca3e58a860f9c489806dad71a5dc65bb5/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f6c65677374612e7376673f7374796c653d706f706f7574) |
0.3.7, 0.5.1 |
https://github.com/tseemann/legsta |
Lyve-SET (includes CG-Pipeline scripts and raxml) ![docker pulls](https://camo.githubusercontent.com/2ecdb3c65aea6c11882cdacbfc2398f9f85353e1e8ac7f443ef290f16a78bb66/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f6c7976657365742e7376673f7374796c653d706f706f7574) |
1.1.4f, 2.0.1 (lyve-SET) |
https://github.com/lskatz/lyve-SET https://github.com/lskatz/CG-Pipeline |
MAFFT ![docker pulls](https://camo.githubusercontent.com/ceca3427692b017d342d21e5173a2d436ef8127d43fbb7ad436494cdbce849bb/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f6d616666742e7376673f7374796c653d706f706f7574) |
7.450 |
https://mafft.cbrc.jp/alignment/software/ |
Mash ![docker pulls](https://camo.githubusercontent.com/d634b8bc5f70ee6c487429a68191de5fbb4416acccf0641a67d31d5906b1765c/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f6d6173682e7376673f7374796c653d706f706f7574) |
2.1, 2.2 |
https://github.com/marbl/Mash |
mashtree ![docker pulls](https://camo.githubusercontent.com/225b51313da38ad967f95aca82b70e2067d8bf2e27f0e3e4a7e2dda057d56a1e/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f6d617368747265652e7376673f7374796c653d706f706f7574) |
0.52.0, 0.57.0, 1.0.4, 1.2.0 |
https://github.com/lskatz/mashtree |
medaka ![docker pulls](https://camo.githubusercontent.com/725bd87cb6dc9b75a628a3acef922d0e48e8abd4e71ee085ce877833451e18e1/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f6d6564616b612e7376673f7374796c653d706f706f7574) |
0.8.1, 1.0.1 |
https://github.com/nanoporetech/medaka |
minimap2 ![docker pulls](https://camo.githubusercontent.com/f5c5fbe4e3e86283f52dd4cde9e017ab4f15e9be0ff323189cc6c7c9f2af212d/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f6d696e696d6170322e7376673f7374796c653d706f706f7574) |
2.17 |
https://github.com/lh3/minimap2 |
mlst ![docker pulls](https://camo.githubusercontent.com/818c3af4ba4926775594dae2c8cc6c16463ad300d28bf341aa4fb36e245378f2/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f6d6c73742e7376673f7374796c653d706f706f7574) |
2.16.2, 2.17.6, 2.19.0 |
https://github.com/tseemann/mlst |
Mugsy ![docker pulls](https://camo.githubusercontent.com/c414afe7009f487435fe6a354c1440e01deb1eab535d83e991c0a0c6323eeebb/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f6d756773792e7376673f7374796c653d706f706f7574) |
1r2.3 |
http://mugsy.sourceforge.net/ |
MultiQC ![docker pulls](https://camo.githubusercontent.com/858dfa72c8b37f01b84eda15f4acea04012d58d0414488a50171f845d8c50b8f/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f6d756c746971632e7376673f7374796c653d706f706f7574) |
1.7, 1.8 |
https://github.com/ewels/MultiQC |
NanoPlot ![docker pulls](https://camo.githubusercontent.com/1813bef80f9f75b1a4e55cba70558beaf1859c87e2bcd1dda00c76766223ff58/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f6e616e6f706c6f742e7376673f7374796c653d706f706f7574) |
1.27.0, 1.29.0, 1.30.1, 1.32.0, 1.33.0 |
https://github.com/wdecoster/NanoPlot |
NCBI AMRFinderPlus ![docker pulls](https://camo.githubusercontent.com/ab548bee88409b449949031beeb7a1aa2fd1e2c6e8196336cbe273d69168f922/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f6e6362692d616d7266696e646572706c75732e7376673f7374796c653d706f706f7574) |
3.1.1b, 3.8.4 |
https://github.com/ncbi/amr |
OrthoFinder ![docker pulls](https://camo.githubusercontent.com/f91a53159646972d52d2dc64703a644599be4c8b1b5a1dbe74865520de7eb2fd/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f6f7274686f66696e6465722e7376673f7374796c653d706f706f7574) |
2.17 |
https://github.com/davidemms/OrthoFinder |
Pangolin ![docker pulls](https://camo.githubusercontent.com/f547dd27e9e6be9c4ebe36f94c9d462bbb1de6909a1f7065037d16fdd2635e83/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f70616e676f6c696e2e7376673f7374796c653d706f706f7574) |
1.1.14, 2.0.4, 2.0.5 |
https://github.com/hCoV-2019/pangolin |
Pilon ![docker pulls](https://camo.githubusercontent.com/4b263c149332ce46ba507f2d628c297a202bfcb874f07aa3eb55416a1c5d5514/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f70696c6f6e2e7376673f7374796c653d706f706f7574) |
1.23.0 |
https://github.com/broadinstitute/pilon |
PlasmidSeeker ![docker pulls](https://camo.githubusercontent.com/334579a8a8a1a730a0214de8ef84c70b7698176c3303ca343ef12f91913b19bd/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f706c61736d69647365656b65722e7376673f7374796c653d706f706f7574) |
1.0 |
https://github.com/bioinfo-ut/PlasmidSeeker |
Prokka ![docker pulls](https://camo.githubusercontent.com/00718cf3d7719bcd0c6cd49f78f10a108f0a7f6b2c18d3393aa5772308b38b2b/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f70726f6b6b612e7376673f7374796c653d706f706f7574) |
1.13.4, 1.14.0, 1.14.5 |
https://github.com/tseemann/prokka |
QUAST ![docker pulls](https://camo.githubusercontent.com/a222219b69ac793fceef06583e75e92622ec59bc7bb8d2cf65389262b20ef612/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f71756173742e7376673f7374796c653d706f706f7574) |
5.0.0, 5.0.2 |
https://github.com/ablab/quast |
racon ![docker pulls](https://camo.githubusercontent.com/9109dd813db89d7adff9bf7324add26c704e56ea1d07d28dbcad68f8c963dd98/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f7261636f6e2e7376673f7374796c653d706f706f7574) |
1.4.3 |
https://github.com/lbcb-sci/racon https://github.com/isovic/racon (ARCHIVED) |
rasusa ![docker pulls](https://camo.githubusercontent.com/0191e63e72d9f305a132e2e881d223e20738a4da526cf44a1e6081f442841a93/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f7261737573612e7376673f7374796c653d706f706f7574) |
0.1.0, 0.2.0, 0.3.0 |
https://github.com/mbhall88/rasusa |
RAxML ![docker pulls](https://camo.githubusercontent.com/540b5e044f325230ad57582dc04e6a52183a341c024a7cfaec7e64a12099e796/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f7261786d6c2e7376673f7374796c653d706f706f7574) |
8.2.12 (RAxML) 0.9.0 (RAxML Next Generation) |
https://github.com/stamatak/standard-RAxML https://github.com/amkozlov/raxml-ng |
Roary ![docker pulls](https://camo.githubusercontent.com/cbf6bc9d35fc80b2c6baa378c63e4db2da1838a4b48fbfda01cb2d411850997a/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f726f6172792e7376673f7374796c653d706f706f7574) |
3.12.0 |
https://github.com/sanger-pathogens/Roary |
SalmID ![docker pulls](https://camo.githubusercontent.com/bd841b95389ecd1f5389b5e33cbf64d39d17d5416ee1278dcadde062fd34afaf/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f73616c6d69642e7376673f7374796c653d706f706f7574) |
0.1.23 |
https://github.com/hcdenbakker/SalmID |
Samtools ![docker pulls](https://camo.githubusercontent.com/c6c2e6a7e851d90793f387aaa78e2a3a7d9f013e00872e1e90cef4f97c907736/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f73616d746f6f6c732e7376673f7374796c653d706f706f7574) |
1.9, 1.10, 1.11 |
https://github.com/samtools/samtools |
SeqSero ![docker pulls](https://camo.githubusercontent.com/543170e840600dcc2889933aabaabc3a36c7f1c79ce86a6ebab17ab72d538252/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f7365717365726f2e7376673f7374796c653d706f706f7574) |
1.0.1 |
https://github.com/denglab/SeqSero |
SeqSero2 ![docker pulls](https://camo.githubusercontent.com/14658f4e7f2cb0268b3f27ba31163b140774117fef12147007103d65c16eac89/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f7365717365726f322e7376673f7374796c653d706f706f7574) |
0.1.0, 1.0.0, 1.0.2, 1.1.0, 1.1.1 |
https://github.com/denglab/SeqSero2/ |
seqtk ![docker pulls](https://camo.githubusercontent.com/4b8fffad4473263999238a1744ba3e96f63b1369b365080328b3b3f8eace03ee/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f736571746b2e7376673f7374796c653d706f706f7574) |
1.3 |
https://github.com/lh3/seqtk |
seqyclean ![docker pulls](https://camo.githubusercontent.com/958a17de0d0101c149a9ab95dc84ecc57451b82c5713c202bbcfafb46453ee51/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f73657179636c65616e2e7376673f7374796c653d706f706f7574) |
1.10.09 |
https://github.com/ibest/seqyclean |
Seroba ![docker pulls](https://camo.githubusercontent.com/0e6e5cda8eed7b844c64bc71b6b223d6f223af1c94ce82debdfd2852d64ce6a2/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f7365726f62612e7376673f7374796c653d706f706f7574) |
1.0.0 |
https://github.com/sanger-pathogens/seroba |
SerotypeFinder ![docker pulls](https://camo.githubusercontent.com/d50c5f7f5be9e8dd37ebf1fd894e1ab0f3e3a9e9d904e3c94ef0198efe04bc31/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f7365726f7479706566696e6465722e7376673f7374796c653d706f706f7574) |
1.1 (I think? Bitbucket repo does not list older versions like the one in this docker image) |
https://bitbucket.org/genomicepidemiology/serotypefinder/ |
Shovill ![docker pulls](https://camo.githubusercontent.com/40261f6757c481a399071fbcbde7689f448891f8a7af913b91943496e7d197da/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f73686f76696c6c2e7376673f7374796c653d706f706f7574) |
1.0.4, 1.1.0 |
https://github.com/tseemann/shovill |
SISTR ![docker pulls](https://camo.githubusercontent.com/ca65863c9c7ba398b23de61203907088d7c0d65fd9ea1dd3f1c9c419ea8d8a62/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f73697374722e7376673f7374796c653d706f706f7574) |
1.0.2 |
https://github.com/peterk87/sistr_cmd |
SKESA ![docker pulls](https://camo.githubusercontent.com/62e61da6555b3f69327a05e3de9025432bbd94452507c09fb8461fc238274f5e/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f736b6573612e7376673f7374796c653d706f706f7574) |
2.3.0, 2.4.0 (gfa_connector & kmercounter included) |
https://github.com/ncbi/SKESA |
Snippy ![docker pulls](https://camo.githubusercontent.com/22aa2a71154e5b43838857cf5f10ac10d353263d15fabbdab73fbdbaa09e06e0/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f736e697070792e7376673f7374796c653d706f706f7574) |
4.4.5, 4.5.1, 4.6.0 |
https://github.com/tseemann/snippy |
snp-dists ![docker pulls](https://camo.githubusercontent.com/3236550892285a6ae6dd897c6040f2017ece5f10cb0b40c8f929a3e4202e2335/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f736e702d64697374732e7376673f7374796c653d706f706f7574) |
0.6.2 |
https://github.com/tseemann/snp-dists |
SNP-sites ![docker pulls](https://camo.githubusercontent.com/7ddf86f897e64267d85987efed78e640d35a12bb26173472815ec45cd14333f0/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f736e702d73697465732e7376673f7374796c653d706f706f7574) |
2.3.3 |
https://github.com/sanger-pathogens/snp-sites |
SPAdes ![docker pulls](https://camo.githubusercontent.com/e059551606bea587b5e99227fc117fbcc9b318fff82553e7d0feaddec8df244b/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f7370616465732e7376673f7374796c653d706f706f7574) |
3.8.2, 3.12.0, 3.13.0, 3.14.0, 3.14.1 |
http://cab.spbu.ru/software/spades/ |
SRA-toolkit ![docker pulls](https://camo.githubusercontent.com/82729a2629da9f8387b01a6fd6f2bb48ebd832dcbdeb097fbcd58c54a8cdfd09/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f737261746f6f6c6b69742e7376673f7374796c653d706f706f7574) |
2.9.2 |
https://github.com/ncbi/sra-tools |
Staramr ![docker pulls](https://camo.githubusercontent.com/db3a8c716534c84d026b8015e349450c250f5fff5a79bb582284c0309dc97a8d/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f73746172616d722e7376673f7374796c653d706f706f7574) |
0.5.1, 0.7.1 |
https://github.com/phac-nml/staramr |
TipToft ![docker pulls](https://camo.githubusercontent.com/9264ef34b5201b7c668175a72067823d2c699f74c6bc179a232cf4c0a217f1de/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f746970746f66742e7376673f7374796c653d706f706f7574) |
1.0.0, 1.0.2 |
https://github.com/andrewjpage/tiptoft |
Trimmomatic ![docker pulls](https://camo.githubusercontent.com/7197edd44d4b618b4310c19dfd88dfab36b766320f63fdb54556b78f95fc0ab7/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f7472696d6d6f6d617469632e7376673f7374796c653d706f706f7574) |
0.38, 0.39 |
http://www.usadellab.org/cms/?page=trimmomatic |
Trycycler ![docker pulls](https://camo.githubusercontent.com/44e7927504df08909d5ea4c13427750a69671a4fe6eb2e0c58873f4c26a7b210/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f7472796379636c65722e7376673f7374796c653d706f706f7574) |
0.3.1, 0.3.2, 0.3.3 |
https://github.com/rrwick/Trycycler |
Unicycler ![docker pulls](https://camo.githubusercontent.com/4ec278325cc762a73b860b605033973e38d7bbad3db0e8a394c859f6437a78c8/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f756e696379636c65722e7376673f7374796c653d706f706f7574) |
0.4.7, 0.4.8 |
https://github.com/rrwick/Unicycler |
VADR ![docker pulls](https://camo.githubusercontent.com/7143646a725401b51b8ea526a4e008858003b971ecd87be267a4b089d6a8406e/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f766164722e7376673f7374796c653d706f706f7574) |
1.1 |
https://github.com/nawrockie/vadr |
VIBRANT ![docker pulls](https://camo.githubusercontent.com/15ad3162fecce18e9d97d105e37f4792cfad5471265861a8a1af098cc1098513/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f76696272616e742e7376673f7374796c653d706f706f7574) |
1.2.1 |
https://github.com/AnantharamanLab/VIBRANT |
VIGOR4 ![docker pulls](https://camo.githubusercontent.com/959b98028a15484f8126b4e2fd7b1f693f75944f844ac90591f4ee4894846aa2/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f7669676f72342e7376673f7374796c653d706f706f7574) |
4.1.20190131 |
https://github.com/JCVenterInstitute/VIGOR4 |
wtdbg2 ![docker pulls](https://camo.githubusercontent.com/a5f3747b4b6b70367ad0d733c152e51c69b987ff7f64138cee0ed9146114ad3d/68747470733a2f2f696d672e736869656c64732e696f2f646f636b65722f70756c6c732f7374617068622f7774646267322e7376673f7374796c653d706f706f7574) |
2.5 |
https://github.com/ruanjue/wtdbg2 |