| abricate; abaum-plasmid |
https://github.com/tseemann/abricate, https://github.com/MehradHamidian/AcinetobacterPlasmidTyping |
| abricate; insaflu |
https://github.com/tseemann/abricate, https://github.com/INSaFLU/INSaFLU/tree/master/static/db/type_identification |
| abricate; vibrio-cholera |
https://github.com/tseemann/abricate |
| agrvate |
https://github.com/VishnuRaghuram94/AgrVATE |
| artic-ncov2019 |
https://github.com/artic-network/ |
| artic-ncov2019-epi2me |
https://github.com/epi2me-labs/wf-artic/ |
| augur |
https://github.com/nextstrain/augur |
| bakta |
https://github.com/oschwengers/bakta |
| basespace_cli |
https://developer.basespace.illumina.com/docs/content/documentation/sdk-samples/ruby-sdk-overview#CopyingandLicense |
| bbtools |
https://github.com/bbushnell/BBTools |
| bcftools |
https://github.com/samtools/bcftools |
| bedtools |
https://github.com/arq5x/bedtools2/ |
| busco |
https://gitlab.com/ezlab/busco |
| centroid |
https://github.com/stjacqrm/centroid/ |
| checkv |
https://bitbucket.org/berkeleylab/checkv/src/master/ |
| clair3 |
https://github.com/HKU-BAL/Clair3 |
| dorado |
https://github.com/nanoporetech/dorado |
| ectyper |
https://github.com/phac-nml/ecoli_serotyping |
| emmtyper |
https://github.com/MDU-PHL/emmtyper |
| emmtypingtool |
https://github.com/ukhsa-collaboration/emm-typing-tool |
| ete4 |
https://github.com/etetoolkit/ete |
| fastp |
https://github.com/OpenGene/fastp |
| fastq-dl |
https://github.com/rpetit3/fastq-dl |
| fastq-scan |
https://github.com/rpetit3/fastq-scan |
| flye |
https://github.com/mikolmogorov/Flye |
| freyja |
https://github.com/andersen-lab/Freyja |
| gambit |
https://github.com/jlumpe/gambit |
| gamma |
https://github.com/rastanton/GAMMA/ |
| gather_samples |
https://github.com/bactopia/bactopia/ |
| genoflu |
https://github.com/USDA-VS/GenoFLU |
| gisaid-cli |
https://github.com/broadinstitute/gisaid-cli |
| google-cloud-cli |
https://github.com/GoogleCloudPlatform/cloud-sdk-docker |
| gubbins |
https://github.com/nickjcroucher/gubbins |
| hicap |
https://github.com/scwatts/hicap |
| iqtree |
https://github.com/iqtree/iqtree1 |
| iqtree2 |
https://github.com/iqtree/iqtree2 |
| irma |
https://github.com/CDCgov/irma |
| ivar |
https://github.com/andersen-lab/ivar/ |
| kaptive |
https://github.com/klebgenomics/Kaptive |
| kleborate |
https://github.com/klebgenomics/Kleborate |
| kmerfinder |
https://bitbucket.org/genomicepidemiology/speciesfinder |
| kraken2 |
https://github.com/DerrickWood/kraken2/ |
| krakentools |
https://github.com/jenniferlu717/KrakenTools |
| krona |
https://github.com/marbl/Krona/tree/master/KronaTools |
| ksnp3 |
https://github.com/kissake/kSNP4 |
| ksnp4 |
https://github.com/kissake/kSNP4 |
| legsta |
https://github.com/tseemann/legsta |
| lissero |
https://github.com/MDU-PHL/lissero |
| lyveset |
https://github.com/lskatz/lyve-SET |
| mashtree |
https://github.com/lskatz/mashtree |
| megahit |
https://github.com/voutcn/megahit |
| meningotype |
https://github.com/MDU-PHL/meningotype |
| mercury |
https://github.com/theiagen/mercury |
| metabuli |
https://github.com/steineggerlab/Metabuli |
| minimap2 |
https://github.com/lh3/minimap2/ |
| mlst |
https://github.com/tseemann/mlst |
| mummer |
https://github.com/mummer4/mummer |
| genotyphi |
https://github.com/typhoidgenomics/genotyphi |
| mykrobe |
https://github.com/Mykrobe-tools/mykrobe |
| mykrobe; sonneityping |
https://github.com/Mykrobe-tools/mykrobe, https://github.com/katholt/sonneityping/ |
| nanoplot |
https://github.com/wdecoster/NanoPlot |
| nanoq |
https://github.com/esteinig/nanoq |
| ncbi-amrfinderplus |
https://github.com/ncbi/amr |
| ncbi-datasets |
https://github.com/theiagen/theiagen_docker_builds/tree/main/ncbi-datasets |
| ncbi-table2asn |
https://www.ncbi.nlm.nih.gov/genbank/table2asn |
| ncbi-tools |
https://github.com/broadinstitute/ncbi-tools |
| nextclade |
https://github.com/nextstrain/nextclade |
| ngmaster |
https://github.com/MDU-PHL/ngmaster |
| pangolin |
https://github.com/cov-lineages/pangolin |
| pasty |
https://github.com/rpetit3/pasty |
| pbptyper |
https://github.com/rpetit3/pbptyper |
| pilon |
https://github.com/broadinstitute/pilon |
| pirate |
https://github.com/SionBayliss/PIRATE |
| plasmidfinder |
https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/ |
| poppunk |
https://github.com/bacpop/PopPUNK |
| porechop |
https://github.com/rrwick/Porechop |
| prokka |
https://github.com/tseemann/prokka |
| python |
https://www.python.org/downloads/release/python-3818/ |
| qualimap-custom-html |
https://bitbucket.org/kokonech/qualimap/commits/branch/master |
| quasitools |
https://github.com/phac-nml/quasitools |
| quast |
https://github.com/ablab/quast |
| rasusa |
https://github.com/mbhall88/rasusa |
| raven |
https://github.com/lbcb-sci/raven |
| referenceseeker |
https://github.com/oschwengers/referenceseeker |
| resfinder |
https://bitbucket.org/genomicepidemiology/resfinder/src/master/ |
| samtools |
https://github.com/samtools/samtools |
| semibin |
https://github.com/BigDataBiology/SemiBin |
| seqkit |
https://github.com/shenwei356/seqkit |
| seqsero2s |
https://github.com/denglab/SeqSero |
| seroba |
https://github.com/GlobalPneumoSeq/seroba |
| serotypefinder |
https://bitbucket.org/genomicepidemiology/serotypefinder/src/master/ |
| shigatyper |
https://github.com/CFSAN-Biostatistics/shigatyper |
| shigeifinder |
https://github.com/LanLab/ShigEiFinder |
| sistr |
https://github.com/phac-nml/sistr_cmd |
| skani |
https://github.com/bluenote-1577/skani |
| skesa |
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 |
https://github.com/ablab/spades |
| spatyper |
https://github.com/HCGB-IGTP/spaTyper |
| sra-human-scrubber |
https://github.com/ncbi/sra-human-scrubber |
| srst2 |
https://github.com/katholt/srst2 |
| staphopia-sccmec |
https://github.com/staphopia/staphopia-sccmec |
| stxtyper |
https://github.com/ncbi/stxtyper |
| tbp-parser |
https://github.com/theiagen/tbp-parser |
| tbprofiler |
https://github.com/jodyphelan/TBProfiler |
| terra_to_ena |
https://github.com/enasequence/ena-bulk-webincli |
| terra-tools |
https://github.com/broadinstitute/terra-tools |
| theiaphylo |
https://github.com/theiagen/theia-phylo-viewer |
| theiavalidate |
https://github.com/theiagen/theiavalidate |
| trimmomatic |
https://github.com/usadellab/Trimmomatic |
| ubuntu |
https://releases.ubuntu.com/jammy/ |
| usher |
https://github.com/yatisht/usher |
| vadr |
https://github.com/NLM-DIR/vadr |
| varpipe_wgs_with_refs |
https://github.com/CDCgov/varpipe_wgs |
| viral-core |
https://github.com/broadinstitute/viral-core |
| virulencefinder |
https://bitbucket.org/genomicepidemiology/virulencefinder/src/master/ |
| vibecheck |
https://github.com/CholGen/Vibecheck |