ABRicate 0.8.7 0.8.13 0.8.13s (+serotypefinder db) 0.9.8 1.0.0 https://github.com/tseemann/abricate ARIBA https://github.com/sanger-pathogens/ariba artic-ncov2019 https://github.com/artic-network/fieldbioinformatics artic-ncov2019-medaka https://github.com/artic-network/artic-ncov2019 artic-ncov2019-nanopolish https://github.com/artic-network/artic-ncov2019 Augur https://github.com/nextstrain/augur Auspice https://github.com/nextstrain/auspice BBTools https://jgi.doe.gov/data-and-tools/bbtools/ bcftools https://github.com/samtools/bcftools bedtools https://bedtools.readthedocs.io/en/latest/ https://github.com/arq5x/bedtools2 BWA https://github.com/lh3/bwa Canu https://canu.readthedocs.io/en/latest/ https://github.com/marbl/canu Canu-Racon 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 https://github.com/stjacqrm/centroid CDC-SPN https://github.com/BenJamesMetcalf/Spn_Scripts_Reference cfsan-snp-pipeline https://github.com/CFSAN-Biostatistics/snp-pipeline Circlator https://github.com/sanger-pathogens/circlator Clustalo http://www.clustal.org/omega/ colorid https://github.com/hcdenbakker/colorid cutshaw-report-env https://github.com/VADGS/CutShaw emm-typing-tool https://github.com/phe-bioinformatics/emm-typing-tool FastANI https://github.com/ParBLiSS/FastANI FastTree http://www.microbesonline.org/fasttree/ FastQC https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ https://github.com/s-andrews/FastQC Filtlong https://github.com/rrwick/filtlong Flye https://github.com/fenderglass/Flye hmmer http://hmmer.org/ iqtree http://www.iqtree.org/ iqtree2 http://www.iqtree.org/ iVar 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 https://github.com/andersen-lab/ivar kma https://bitbucket.org/genomicepidemiology/kma/ Kraken 1.0 1.0.0_wslh_signed 1.1.1 1.1.1 (no database) https://github.com/DerrickWood/kraken Kraken2 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) https://github.com/DerrickWood/kraken2 kSNP3 https://sourceforge.net/projects/ksnp/ legsta https://github.com/tseemann/legsta Lyve-SET (includes CG-Pipeline scripts and raxml) https://github.com/lskatz/lyve-SET https://github.com/lskatz/CG-Pipeline MAFFT https://mafft.cbrc.jp/alignment/software/ Mash https://github.com/marbl/Mash mashtree https://github.com/lskatz/mashtree medaka https://github.com/nanoporetech/medaka metaphlan 3.0.3-no-db (no database) 3.0.3 (~3GB db) https://github.com/biobakery/MetaPhlAn/tree/3.0 minimap2 https://github.com/lh3/minimap2 mlst https://github.com/tseemann/mlst Mugsy http://mugsy.sourceforge.net/ MultiQC https://github.com/ewels/MultiQC NanoPlot 1.27.0 1.29.0 1.30.1 1.32.0 1.33.0 https://github.com/wdecoster/NanoPlot NCBI AMRFinderPlus 3.1.1b 3.8.4 3.8.28 3.9.3 3.9.8 3.10.1 https://github.com/ncbi/amr OrthoFinder https://github.com/davidemms/OrthoFinder Pangolin 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 https://github.com/hCoV-2019/pangolin (archived) https://github.com/cov-lineages/pangolin https://github.com/cov-lineages/pangoLEARN https://github.com/cov-lineages/lineages parallel-perl https://www.gnu.org/software/parallel Pilon https://github.com/broadinstitute/pilon PlasmidSeeker https://github.com/bioinfo-ut/PlasmidSeeker Prokka https://github.com/tseemann/prokka QUAST https://github.com/ablab/quast racon https://github.com/lbcb-sci/racon https://github.com/isovic/racon (ARCHIVED)rasusa https://github.com/mbhall88/rasusa RAxML 8.2.12 (RAxML) and 0.9.0 (RAxML Next Generation) https://github.com/stamatak/standard-RAxML https://github.com/amkozlov/raxml-ng Roary https://github.com/sanger-pathogens/Roary SalmID https://github.com/hcdenbakker/SalmID Samtools https://github.com/samtools/samtools SeqSero https://github.com/denglab/SeqSero SeqSero2 0.1.0 1.0.0 1.0.2 1.1.0 1.1.1 1.2.1 https://github.com/denglab/SeqSero2/ seqtk https://github.com/lh3/seqtk seqyclean https://github.com/ibest/seqyclean Seroba 1.0.0 1.0.2 1.0.2_wslh_signed https://github.com/sanger-pathogens/seroba SerotypeFinder 1.1 (perl version) 2.0.1 (python version) https://bitbucket.org/genomicepidemiology/serotypefinder/ Shovill https://github.com/tseemann/shovill SISTR https://github.com/phac-nml/sistr_cmd SKESA 2.3.0 2.4.0 (gfa_connector
& kmercounter
included) https://github.com/ncbi/SKESA Snippy https://github.com/tseemann/snippy snp-dists https://github.com/tseemann/snp-dists SNP-sites https://github.com/sanger-pathogens/snp-sites SPAdes 3.8.2 3.12.0 3.13.0 3.14.0 3.14.1 3.15.0 3.15.1 3.15.2 https://github.com/ablab/spades http://cab.spbu.ru/software/spades/ SRA-toolkit https://github.com/ncbi/sra-tools Staramr https://github.com/phac-nml/staramr TipToft https://github.com/andrewjpage/tiptoft Treemmer [ ](https://hub.docker.com/r/staphb/t