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This repository contains the Dockerfiles and other assorted files necessary for building Docker images for a variety of programs used by members of the StaPH-B (State Public Health Lab Bioinformatics) consortium. The purpose of this repository is to provide a centralized location for Docker images that is easily accessible for users, with clear documentation on how the containers were built and how to use them.

There are several community projects that create and share containers for bioinformatic tools. This repository contains the Dockerfiles and other assorted files necessary for building Docker images for a variety of tools used by members of the StaPH-B (State Public Health Lab Bioinformatics) consortium. The purpose of this repository is to provide a centralized location for Docker images that is easily accessible for users, with clear documentation on how the containers were built and how to use them.

This is a community resource, built and maintined by users from varied backgrounds and expertise levels. As such, we have provided some templates for contributing to this repository. If you would like to add a Docker image or improve upon the existing images, please fork the repository, make your changes/additions, and submit a pull request. If you are having an issue with an existing image, please submit an issue. We welcome any and all feedback!

See more details on how to contribute here

Docker image repositories & hosting

We host all of our docker images on two different repositories:

  1. Dockerhub - https://hub.docker.com/r/staphb/
  2. Quay.io - https://quay.io/organization/staphb/

The development process of creating a new image is summarized as follows:

graph TD
     A[fork staphb/docker-builds repo]-->B[create tool/version directory]
     B-->C[create readme]
     B-->D[create dockerfile]
     D-->G[create app and test layers]
     A-->E[add License to Program_Licenses.md]
     A-->F[add tool to list in this readme]
     E-->H[submit PR]
     F-->H
     G-->H
     C-->H
     H-->I{build to test}
     I--success-->J[PR merged and docker image pushed to dockerhub and quay]
     I--failure-->K[edit dockerfile]
     K-->I

User Guide

The StaPH-B Docker User Guide was created to outline methods and best practices for using and developing docker containers. There are chapters for:

Summarized usage guide for docker

# Build a docker image to the 'test' layer
docker build --tag tool:test --target test <directory to Dockerfile>
docker build --tag samtools:test --target test samtools/1.15

# Download a docker image from dockerhub (most tools have a 'latest' version tag)
docker pull staphb/tool:version
docker pull staphb/shigatyper:2.0.2

# Run the container (don't forget to mount your volumes!)
docker run --rm -u $(id -u):$(id -g) -v <local directory>:/data tool:version <command>
docker run --rm -u $(id -u):$(id -g) -v $(pwd)/amrfinder_test_files:/data amrfinder:3.10 amrfinder --nucleotide 2021CK-01854_contigs.fa --threads 20 --name 2021CK-01854 --output /data/2021CK-01854.txt --organism Klebsiella

Further documentation can be found at docs.docker.com

Templates

Several template files are provided. These are intended to be copied and edited by contributors.

  1. dockerfile-template/Dockerfile is the basic template useful for most images
  2. dockerfile-template/Dockerfile_mamba is a basic template for using the micromamba base image
  3. dockerfile-template/README.md is a basic readme file template to assist others in using the image

What about Singularity?

For many people, Docker is not an option, but Singularity is. Most Docker containers are compatible with Singularity and can easily be converted to Singularity format. Please see the User Guide for instructions on how to download docker images from dockerhub and how to run them using Singularity. We've worked hard to ensure that our containers are compatibile with Singularity, but if you find one that isn't, please leave an issue and let us know!

Summarized usage guide for singularity

# Pulling a container from dockerhub (creates a file)
singularity pull --name <name of singularity file> docker://staphb/bbtools:38.96
singularity pull --name staphb-bbtools-38.96.simg docker://staphb/bbtools:38.96

# Running the container (don't forget to mount your volumes!)
singularity exec --bind <local directory>:/data <name of singularity file> <command>
singularity exec --bind $(pwd)/fastq:/data staphb-bbtools-38.96.simg bbduk.sh in1=sample1_R1.fastq.gz in2=sample1_R2.fastq.gz out1=bbduk/sample1_rmphix_R1.fastq.gz out2=bbduk/sample1_rmphix_R2.fastq.gz outm=bbduk/sample1.matched_phix.fq ref=/opt/bbmap/resources/phix174_ill.ref.fa.gz stats=bbduk/sample1.phix.stats.txt threads=4

Further documentation can be found at docs.sylabs.io

Training

Logs

In November 2020, Docker began to implement pull rate limits for images hosted on dockerhub. This limits the number of docker pull's per time period (e.g. anonymous users allowed 100 pulls per six hours). We applied and were approved for Docker's "Open Source Program," which should have removed the pull rate limits for all staphb docker images! 🎉 🥳 If you encounter an error such as ERROR: toomanyrequests: Too Many Requests. or You have reached your pull rate limit. You may increase the limit by authenticating and upgrading: https://www.docker.com/increase-rate-limits. , please let us know by submitting an issue.

A huge thank you goes to the folks at Docker for supporting our efforts to distribute & share critical tools for public health bioinformatics. This has been especially important during the COVID-19 global pandemic, as many of these tools are used to conduct genomic surveillance on the SARS-CoV-2 virus as well as other important pathogens of public health concern.

To learn more about the docker pull rate limits and the open source software program, please see these blog posts (1, 2, and 3) and Docker documentation (1).

NOTE: In the table below, we do not provide individual links to the various tools on quay.io, please visit the above quay.io link to find all of our docker images.

Available Docker images

SoftwareVersionLink
ABRicate <br/> docker pulls<ul><li>0.8.7</li><li>0.8.13</li><li>0.8.13s (+serotypefinder db)</li><li>0.9.8</li><li>1.0.0</li><li>1.0.1 (+ A. baumannii plasmid typing db)</li><li>1.0.1 (+ InsaFlu db)</li><li>1.0.1 (+ Vibrio cholerae db)</li></ul>https://github.com/tseemann/abricate
ACI <br/> docker pulls<ul><li>1.4.20240116</li></ul>https://github.com/erinyoung/ACI
ANIclustermap <br/> docker pulls<ul><li>1.3.0</li><li>1.4.0</li></ul>https://github.com/moshi4/ANIclustermap
any2fasta <br/> docker pulls<ul><li>0.4.2</li></ul>https://github.com/tseemann/any2fasta
ARIBA <br/> docker pulls<ul><li>2.14.4</li><li>2.14.6</li><li>2.14.7</li></ul>https://github.com/sanger-pathogens/ariba
artic <br/> docker pulls<ul><li>1.2.4-1.11.1 (artic-medaka)</li><li>1.2.4-1.12.0 (artic-medaka)</li></ul>https://github.com/artic-network/fieldbioinformatics
artic-ncov2019 <br/> docker pulls<ul><li>1.3.0</ul>https://github.com/artic-network/fieldbioinformatics
artic-ncov2019-epi2me <br/> docker pulls<ul><li>0.3.10</ul>https://github.com/epi2me-labs/wf-artic
artic-ncov2019-medaka <br/> docker pulls<ul><li>1.1.0</ul>https://github.com/artic-network/artic-ncov2019
artic-ncov2019-nanopolish <br/> docker pulls<ul><li>1.1.0</ul>https://github.com/artic-network/artic-ncov2019
assembly_snptyper <br/> docker pulls<ul><li>0.1.1</li></ul>https://github.com/boasvdp/assembly_snptyper
Augur <br/> docker pulls<ul><li>6.3.0</li><li>7.0.2</li><li>8.0.0</li><li>9.0.0</li><li>16.0.3</li><li>24.2.2</li><li>24.2.3</li><li>24.3.0</li><li>24.4.0</li><li>26.0.0</li></ul>https://github.com/nextstrain/augur
Auspice <br/> docker pulls<ul><li>2.12.0</li></ul>https://github.com/nextstrain/auspice
bakta <br/> docker pulls<ul><li>1.9.2</li><li>1.9.2-light</li><li>1.9.3</li><li>1.9.3-light</li><li>1.9.4</li><li>1.9.4-5.1-light</ul>https://github.com/oschwengers/bakta
bandage <br/> docker pulls<ul><li>0.8.1</li></ul>https://rrwick.github.io/Bandage/
BBTools <br/> docker pulls<ul><li>38.76</li><li>38.86</li><li>38.95</li><li>38.96</li><li>38.97</li><li>38.98</li><li>38.99</li><li>39.00</li><li>39.01</li><li>39.06</li><li>39.10</li></ul>https://jgi.doe.gov/data-and-tools/bbtools/
bcftools <br/> docker pulls<ul><li>1.10.2</li><li>1.11</li><li>1.12</li><li>1.13</li><li>1.14</li><li>1.15</li><li>1.16</li><li>1.17</li><li>1.18</li><li>1.19</li><li>1.20</li><li>1.20.c</li><li>1.21</li></ul>https://github.com/samtools/bcftools
bedtools <br/> docker pulls<ul><li>2.29.2</li><li>2.30.0</li><li>2.31.0</li><li>2.31.1</li></ul>https://bedtools.readthedocs.io/en/latest/ <br/>https://github.com/arq5x/bedtools2
berrywood-report-env <br/> docker pulls<ul><li>1.0</li></ul>none
blast+ <br/> docker pulls<ul><li>2.13.0</li><li>2.14.0</li><li>2.14.1</li><li>2.15.0</li><li>2.16.0</li></ul>https://www.ncbi.nlm.nih.gov/books/NBK279690/
bowtie2 <br/> docker pulls<ul><li>2.4.4</li><li>2.4.5</li><li>2.5.1</li><li>2.5.3</li><li>2.5.4</li></ul>http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml <br/>https://github.com/BenLangmead/bowtie2
Bracken <br/> docker pulls<ul><li>2.9</li></ul>https://ccb.jhu.edu/software/bracken/index.shtml?t=manual <br/>https://github.com/jenniferlu717/Bracken
BUSCO <br/> docker pulls<ul><li>5.4.7</li><li>5.6.1</li><li>5.6.1-prok-bacteria_odb10_2024-01-08</li><li>5.7.1</li><li>5.7.1-prok-bacteria_odb10_2024-01-08</li><li>5.8.0</li><li>5.8.0-prok-bacteria_odb10_2024-01-08</li></ul>https://busco.ezlab.org/busco_userguide.html <br/>https://gitlab.com/ezlab/busco
BWA <br/> docker pulls<ul><li>0.7.17</li><li>0.7.18</li></ul>https://github.com/lh3/bwa
Canu <br/> docker pulls<ul><li>2.0</li><li>2.1.1</li><li>2.2</li></ul>https://canu.readthedocs.io/en/latest/ <BR/> https://github.com/marbl/canu
Canu-Racon <br/> docker pulls<ul><li>1.7.1 (Canu), 1.3.1 (Racon), 2.13 (minimap2)</li><li>1.9 (Canu), 1.4.3 (Racon), 2.17 (minimap2)</li><li>1.9i (Canu), 1.4.3 (Racon), 2.17 (minimap2), (+racon_preprocess.py)</li><li>2.0 (Canu), 1.4.3 (Racon), 2.17 (minimap2)</li></ul>https://canu.readthedocs.io/en/latest/ <br/> https://github.com/lbcb-sci/racon <br/> https://github.com/isovic/racon (ARCHIVED) <br/> https://lh3.github.io/minimap2/
centroid <br/> docker pulls<ul><li>1.0.0</li></ul>https://github.com/stjacqrm/centroid
CDC-SPN <br/> docker pulls<ul><li>0.1 (no version)</li></ul>https://github.com/BenJamesMetcalf/Spn_Scripts_Reference
cfsan-snp-pipeline <br/> docker pulls<ul><li>2.0.2</li> <li>2.2.1</li> </ul>https://github.com/CFSAN-Biostatistics/snp-pipeline
CheckM <br/> docker pulls<ul><li>1.2.2</li><li>1.2.3</li></ul>https://github.com/Ecogenomics/CheckM
CheckM2 <br/> docker pulls<ul><li>1.0.2</li></ul>https://github.com/chklovski/CheckM2
CheckV <br/> docker pulls<ul><li>1.0.3</li></ul>https://bitbucket.org/berkeleylab/checkv/
Circlator <br/> docker pulls<ul><li>1.5.6</li><li>1.5.5</li></ul>https://github.com/sanger-pathogens/circlator
Circos <br/> docker pulls<ul><li>0.69-9</li></ul>https://circos.ca/
CirculoCov <br/> docker pulls<ul><li>0.1.20240104</li></ul>https://github.com/erinyoung/CirculoCov
Clair3 <br/> docker pulls<ul><li>1.0.9</li><li>1.0.10</li></ul>https://github.com/HKU-BAL/Clair3
Clustalo <br/> docker pulls<ul><li>1.2.4</li></ul>http://www.clustal.org/omega/
colorid <br/> docker pulls<ul><li>0.1.4.3</li></ul>https://github.com/hcdenbakker/colorid
cutshaw-report-env <br/> docker pulls<ul><li>1.0.0</li></ul>https://github.com/VADGS/CutShaw
datasets-sars-cov-2 <br/> docker pulls<ul><li>0.6.2</li><li>0.6.3</li><li>0.7.2</li></ul>https://github.com/CDCgov/datasets-sars-cov-2
diamond <br/> docker pulls<ul><li>2.1.9</li><li>2.1.10</li></ul>https://github.com/bbuchfink/diamond
dnaapler <br/> docker pulls<ul><li>0.1.0</li></ul> <ul><li>0.4.0</li><li>0.5.0</li><li>0.5.1</li><li>0.7.0</li><li>0.8.0</li><li>0.8.1</li></ul>https://github.com/gbouras13/dnaapler
dorado <br/> docker pulls<ul><li>0.8.0</li><li>0.8.3</li></ul>https://github.com/nanoporetech/dorado
dragonflye <br/> docker pulls<ul><li>1.0.14</li><li>1.1.1</li><li>1.1.2</li><li>1.2.0</li><li>1.2.1</li></ul>https://github.com/rpetit3/dragonflye
Dr. PRG <br/> docker pulls<ul><li>0.1.1</li></ul>https://mbh.sh/drprg/
DSK <br/> docker pulls<ul><li>0.0.100</li><li>2.3.3</li></ul>https://gatb.inria.fr/software/dsk/
el_gato <br/> docker pulls<ul><li>1.15.2</li><li>1.18.2</li><li>1.19.0</li><li>1.20.0</li><li>1.20.1</li></ul>https://github.com/appliedbinf/el_gato
emboss <br/> docker pulls<ul><li>6.6.0 (no version)</li></ul>http://emboss.sourceforge.net
emmtyper <br/> docker pulls<ul><li>0.2.0</li></ul>https://github.com/MDU-PHL/emmtyper
emm-typing-tool <br/> docker pulls<ul><li>0.0.1 (no version)</li></ul>https://github.com/phe-bioinformatics/emm-typing-tool
EToKi <br/> docker pulls<ul><li>1.2.1</li></ul>https://github.com/zheminzhou/EToKi
FastANI <br/> docker pulls<ul><li>1.1</li><li>1.32</li><li>1.33</li><li>1.33 + RGDv2</li><li>1.34</li><li>1.34 + RGDv2</li></ul>https://github.com/ParBLiSS/FastANI
fasten <br/> docker pulls<ul><li>0.7.2</li><li>0.8.1</li></ul>https://github.com/lskatz/fasten
Fastp <br/> docker pulls<ul><li>0.23.2</li><li>0.23.4</li></ul>http://opengene.org/fastp/ <br/> https://github.com/OpenGene/fastp
FastTree <br/> docker pulls<ul><li>2.1.11</li></ul>http://www.microbesonline.org/fasttree/
FastQC <br/> docker pulls<ul><li>0.11.8</li><li>0.11.9</li><li>0.12.1</li></ul>https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ <br/> https://github.com/s-andrews/FastQC
fastq-scan <br/> docker pulls<ul><li>0.4.3</li><li>0.4.4</li><li>1.0.0</li><li>1.0.1</li></ul>https://github.com/rpetit3/fastq-scan
Freebayes <br/> docker pulls<ul><li>1.3.6</li><li>1.3.7</li><li>1.3.7</li><li>1.3.7</li></ul>https://github.com/freebayes/freebayes
Filtlong <br/> docker pulls<ul><li>0.2.0</li><li>0.2.1</li></ul>https://github.com/rrwick/filtlong
FLASH <br/> docker pulls<ul><li>1.2.11</li></ul>http://ccb.jhu.edu/software/FLASH
Flye <br/> docker pulls<ul><li>2.5</li><li>2.7</li><li>2.8</li><li>2.9</li><li>2.9.1</li><li>2.9.2</li><li>2.9.3</li><li>2.9.4</li><li>2.9.5</li></ul>https://github.com/fenderglass/Flye
Freyja <br/> docker pulls<ul><li>1.2</li><li>1.2.1</li><li>1.3.1</li><li>1.3.2</li><li>1.3.4</li><li>1.3.7</li><li>1.3.8</li><li>1.3.9</li><li>1.3.10</li><li>1.3.11</li><li>1.3.12</li><li>1.4.2</li><li>1.4.3</li><li>1.4.4</li><li>1.4.5</li><li>1.4.7</li><li>1.4.8</li><li>1.4.9</li><li>1.5.0</li><li>1.5.1</li><li>1.5.2</li></ul>https://github.com/andersen-lab/Freyja
GAMBIT <br/> docker pulls<ul><li>0.3.0</li><li>0.4.0</li><li>0.5.0</li><li>1.0.0</li></ul>https://github.com/jlumpe/gambit
GAMMA <br/> docker pulls<ul><li>1.4</li><li>2.1</li><li>2.2</li></ul>https://github.com/rastanton/GAMMA/
GenoFLU <br/> docker pulls<ul><li>1.03</li></ul>https://github.com/USDA-VS/GenoFLU
geNomad <br/> docker pulls<ul><li>1.7.4</li><li>1.8.0</li><li>1.8.1</li></ul>https://github.com/apcamargo/genomad
GenoVi <br/> docker pulls<ul><li>0.2.16</li></ul>https://github.com/robotoD/GenoVi
gfastats <br/> docker pulls<ul><li>1.3.6</li><li>1.3.7</li></ul>https://github.com/vgl-hub/gfastats
Gubbins <br/> docker pulls<ul><li>3.3.3</li><li>3.3.4</li><li>3.3.5</li></ul>https://github.com/nickjcroucher/gubbins
heatcluster <br/> docker pulls<ul><li>1.0.2c</li></ul>https://github.com/DrB-S/heatcluster/tree/main
hmmer <br/> docker pulls<ul><li>3.3</li><li>3.3.2</li><li>3.4</li></ul>http://hmmer.org/
homopolish <br/> docker pulls<ul><li>0.4.1</li></ul>https://github.com/ythuang0522/homopolish/
htslib <br/> docker pulls<ul><li>1.14</li><li>1.15</li><li>1.16</li><li>1.17</li><li>1.18</li><li>1.19</li><li>1.20</li><li>1.20.c</li><li>1.21</li></ul>https://www.htslib.org/
Integron Finder <br/> docker pulls<ul><li>2.0.5</li></ul>https://github.com/gem-pasteur/Integron_Finder
iqtree <br/> docker pulls<ul><li>1.6.7</li></ul>http://www.iqtree.org/
iqtree2 <br/> docker pulls<ul><li>2.1.2</li><li>2.2.2.2</li><li>2.2.2.6</li><li>2.2.2.7</li><li>2.3.1</li><li>2.3.4</li><li>2.3.6</li></ul>http://www.iqtree.org/
IPA <br/> docker pulls<ul><li>1.8.0</li></ul>https://github.com/PacificBiosciences/pbipa
IRMA <br/> docker pulls<ul><li>1.0.2</li><li>1.0.3</li><li>1.1.2</li><li>1.1.3</li><li>1.1.4</li></ul>https://wonder.cdc.gov/amd/flu/irma/
isPcr <br/> docker pulls<ul><li>33</li></ul>https://users.soe.ucsc.edu/~kent/
iVar <br/> docker pulls<ul><li>1.1</li><li>1.1 (+SARS-CoV2 reference)</li><li>1.2.1</li><li>1.2.1 (+SC2 ref)</li><li>1.2.2 (+SC2 ref and artic bedfiles)</li><li>1.3</li><li>1.3.1</li><li>1.3.2</li><li>1.4.1</li><li>1.4.2</li><li>1.4.3</li></ul>https://github.com/andersen-lab/ivar
Jasmine <br/> docker pulls<ul><li>2.0.0</li></ul>https://github.com/PacificBiosciences/jasmine
Kaptive <br/> docker pulls<ul><li>2.0.0</li><li>2.0.3</li><li>2.0.5</li><li>2.0.8</li><li>3.0.0b6</li></ul>https://github.com/klebgenomics/Kaptive
Kleborate <br/> docker pulls<ul><li>2.0.4</li><li>2.1.0</li><li>2.2.0</li><li>2.3.2</li><li>2.3.2-2023-05</li><li>2.4.1</li><li>3.1.2</li></ul>https://github.com/katholt/Kleborate/ <br/> https://github.com/katholt/Kaptive/
kma <br/> docker pulls<ul><li>1.2.21</li><li>1.4.10 (no database)</li><li>1.4.14 (no database)</li></ul>https://bitbucket.org/genomicepidemiology/kma/
Kraken <br/> docker pulls<ul><li>1.0</li><li>1.1.1</li><li>1.1.1 (no database)</li></ul>https://github.com/DerrickWood/kraken
Kraken2 <br/> docker pulls<ul><li>2.0.8-beta (no database)</li><li>2.0.8-beta (MiniKraken2_v1_8GB db)</li><li>2.0.8-beta_hv (human + virus db)</li><li>2.0.9-beta (no db)</li><li>2.0.9-beta (Minikraken v2 RefSeq: bacteria, archaea, viral, and human 8GB db)</li><li>2.1.0 (no db)</li><li>2.1.1 (no db)</li><li>2.1.2 (no db)</li><li>2.1.3 (no db)</li></ul>https://github.com/DerrickWood/kraken2
KrakenTools <br/> docker pulls<ul><li>d4a2fbe</li></ul>https://github.com/jenniferlu717/KrakenTools
KrakenUniq <br/> docker pulls<ul><li>1.0.4 (no database)</li></ul>https://github.com/fbreitwieser/krakenuniq
kSNP3 <br/> docker pulls<ul><li>3.1</li></ul>https://sourceforge.net/projects/ksnp/
kSNP4 <br/> docker pulls<ul><li>4.0</li><li>4.1</li></ul>https://sourceforge.net/projects/ksnp/
label <br/> docker pulls<ul><li>0.6.4</li></ul>https://wonder.cdc.gov/amd/flu/label
legsta <br/> docker pulls<ul><li>0.3.7</li><li>0.5.1</li></ul>https://github.com/tseemann/legsta
liftoff <br/> docker pulls<ul><li>1.6.3</li></ul>https://github.com/agshumate/Liftoff
lima <br/> docker pulls<ul><li>2.9.0</li><li>2.9.0+Rscripts</li></ul>https://github.com/PacificBiosciences/barcoding
longshot <br/> docker pulls<ul><li>0.4.5</li><li>1.0.0</li></ul>https://github.com/pjedge/longshot
Lyve-SET (includes CG-Pipeline scripts and raxml) <br/> docker pulls<ul><li>1.1.4f</li><li>2.0.1</li></ul>https://github.com/lskatz/lyve-SET https://github.com/lskatz/CG-Pipeline
MAFFT <br/> docker pulls<ul><li>7.450</li><li>7.475</li><li>7.505</li><li>7.520</li><li>7.526</li></ul>https://mafft.cbrc.jp/alignment/software/
Mash <br/> docker pulls<ul><li>2.1</li><li>2.2</li><li>2.3</li></ul>https://github.com/marbl/Mash
mashtree <br/> docker pulls<ul><li>0.52.0</li><li>0.57.0</li><li>1.0.4</li><li>1.2.0</li><li>1.4.6</li></ul>https://github.com/lskatz/mashtree
MaSuRCA <br/> docker pulls<ul><li>4.0.8</li><li>4.0.9</li><li>4.1.0</li></ul>https://github.com/alekseyzimin/masurca
medaka <br/> docker pulls<ul><li>0.8.1</li><li>1.0.1</li><li>1.2.0</li><li>2.0.0</li><li>2.0.1</li></ul>https://github.com/nanoporetech/medaka
metaphlan <br/> docker pulls<ul><li>3.0.3-no-db (no database)</li><li> 3.0.3 (~3GB db)</li><li>4.1.0 (no database)</li><li>4.1.1 (no database)</li></ul>https://github.com/biobakery/MetaPhlAn
MIDAS <br/> docker pulls<ul><li>1.3.2 (no database)</li>https://github.com/snayfach/MIDAS
minimap2 <br/> docker pulls<ul><li>2.17</li><li>2.18</li><li>2.21</li><li>2.22</li><li>2.23</li><li>2.24</li><li>2.25</li><li>2.26</li><li>2.27</li><li>2.28</li></ul>https://github.com/lh3/minimap2
minipolish <br/> docker pulls<ul><li>0.1.3</li></ul>https://github.com/rrwick/Minipolish
mlst <br/> docker pulls<ul><li>2.16.2</li><li>2.17.6</li><li>2.19.0</li><li>2.22.0</li><li>2.22.1</li><li>2.23.0</li><li>2.23.0-2023-07 (databases updated July 2023)</li><li>2.23.0-2023-08 (databases updated Aug 2023)</li><li>2.23.0-2024-01 (databases updated Jan 2024)</li><li>2.23.0-2024-03 (databases updated March 2024)</li></ul>https://github.com/tseemann/mlst
Mugsy <br/> docker pulls<ul><li>1r2.3</li></ul>http://mugsy.sourceforge.net/
MultiQC <br/> docker pulls<ul><li>1.7</li><li>1.8</li><li>1.18</li><li>1.19</li><li>1.22.2</li><li>1.22.3</li><li>1.25</li></ul>https://github.com/MultiQC/MultiQC
Mummer <br/> docker pulls<ul><li>4.0.0</li><li>4.0.0 + RGDv2</li><li>4.0.0 + RGDv2 + gnuplot</li></ul>https://github.com/mummer4/mummer
Mykrobe + Genotyphi + sonneityping <br/> docker pulls<ul><li>0.11.0 (Mykrobe) & 1.9.1 (Genotyphi) </li><li>0.12.1 (Mykrobe) & 1.9.1 (Genotyphi) & v20210201 (sonneityping) </li><li>0.12.1 (Mykrobe) & 2.0 (Genotyphi) & v20210201 (sonneityping) </li><li>0.12.2 (Mykrobe) & 2.0 (Genotyphi) & v20210201 (sonneityping)</li><li>0.13.0</li></ul>https://github.com/Mykrobe-tools/mykrobe <br/> https://github.com/typhoidgenomics/genotyphi <br/> https://github.com/katholt/sonneityping
NanoPlot <br/> docker pulls<ul><li>1.27.0</li><li>1.29.0</li><li>1.30.1</li><li>1.32.0</li><li>1.33.0</li><li>1.40.0</li><li>1.41.6</li><li>1.42.0</li></ul>https://github.com/wdecoster/NanoPlot
ngmaster <br/> docker pulls<ul><li>0.5.8</li><li>1.0.0</li></ul>https://github.com/MDU-PHL/ngmaster
NCBI Datasets <br/> docker pulls<details><summary> Click to see all datasets versions </summary> datasets versions <ul><li>13.31.0</li><li>13.35.0</li><li>13.43.2</li><li>14.0.0</li><li>14.3.0</li><li>14.7.0</li><li>14.13.2</li><li>14.20.0</li><li>14.27.0</li><li>15.1.0</li><li>15.2.0</li><li>15.11.0</li><li>15.27.1</li><li>15.31.0</li><li>16.2.0</li><li>16.8.1</li><li>16.10.3</li><li>16.15.0</li><li>16.22.1</li><li>16.30.0</li><li>16.35.0</li></ul>https://github.com/ncbi/datasets <br/>https://www.ncbi.nlm.nih.gov/datasets/docs/v1/
NCBI AMRFinderPlus <br/> docker pullsAMRFinderPlus & database verion <details><summary> Click to see AMRFinderplus v3.11.4 and older versions! </summary> <ul><li>3.1.1b</li><li>3.8.4</li><li>3.8.28</li><li>3.9.3</li><li>3.9.8</li><li>3.10.1</li><li>3.10.5</li><li>3.10.16</li><li>3.10.20</li><li>3.10.24</li><li>3.10.30</li><li>3.10.36</li><li>3.10.42</li><li>3.11.2 & 2022-12-19.1</li><li>3.11.2 & 2023-02-23.1</li><li>3.11.4 & 2023-02-23.1</li></ul> </details> <ul><li>3.11.8 & 2023-02-23.1</li><li>3.11.11 & 2023-04-17.1</li><li>3.11.14 & 2023-04-17.1</li><li>3.11.17 & 2023-07-13.2</li><li>3.11.18 & 2023-08-08.2</li><li>3.11.20 & 2023-09-26.1</li><li>3.11.26 & 2023-11-15.1</li><li>3.12.8 & 2024-01-31.1</li><li>3.12.8 & 2024-05-02.2</li><li>3.12.8 & 2024-07-22.1</li><li>4.0.3 & 2024-10-22.1 (includes stxtyper)</li></ul>https://github.com/ncbi/amr
NCBI table2asn <br/> docker pulls<ul><li>1.26.678</li><li>1.28.943</li><li>1.28.1021</li></ul>https://www.ncbi.nlm.nih.gov/genbank/table2asn/ <br/>https://ftp.ncbi.nlm.nih.gov/asn1-converters/versions/2022-06-14/by_program/table2asn/
ONTime <br/> docker pulls<ul><li>0.2.3</li><li>0.3.1</li></ul>https://github.com/mbhall88/ontime
OrthoFinder <br/> docker pulls<ul><li>2.17</li></ul>https://github.com/davidemms/OrthoFinder
Panaroo <br/> docker pulls<ul><li>1.2.10</li><li>1.3.4</li><li>1.5.0</li></ul>(https://hub.docker.com/r/staphb/panaroo)
pango_aliasor <br/> docker pulls<ul><li>0.3.0</li></ul>https://github.com/corneliusroemer/pango_aliasor
Pangolin <br/> docker pulls<details><summary> Click to see Pangolin v4.2 and older versions! </summary> Pangolin version & pangoLEARN data release date <ul><li>1.1.14</li><li>2.0.4 & 2020-07-20</li><li>2.0.5 & 2020-07-20</li><li>2.1.1 & 2020-12-17</li><li>2.1.3 & 2020-12-17</li><li>2.1.6 & 2021-01-06</li><li>2.1.7 & 2021-01-11</li><li>2.1.7 & 2021-01-20</li><li>2.1.8 & 2021-01-22</li><li>2.1.10 & 2021-02-01</li><li>2.1.11 & 2021-02-01</li><li>2.1.11 & 2021-02-05</li><li>2.2.1 & 2021-02-06</li><li>2.2.2 & 2021-02-06</li><li>2.2.2 & 2021-02-11</li><li>2.2.2 & 2021-02-12</li><li>2.3.0 & 2021-02-12</li><li>2.3.0 & 2021-02-18</li><li>2.3.0 & 2021-02-21</li><li>2.3.2 & 2021-02-21</li><li>2.3.3 & 2021-03-16</li><li>2.3.4 & 2021-03-16</li><li>2.3.5 & 2021-03-16</li><li>2.3.6 & 2021-03-16</li><li>2.3.6 & 2021-03-29</li><li>2.3.8 & 2021-04-01</li><li>2.3.8 & 2021-04-14</li><li>2.3.8 & 2021-04-21</li><li>2.3.8 & 2021-04-23</li><li>2.4 & 2021-04-28</li><li>2.4.1 & 2021-04-28</li><li>2.4.2 & 2021-04-28</li><li>2.4.2 & 2021-05-10</li><li>2.4.2 & 2021-05-11</li><li>2.4.2 & 2021-05-19</li><li>3.0.5 & 2021-06-05</li><li>3.1.3 & 2021-06-15</li><li>3.1.5 & 2021-06-15</li><li>3.1.5 & 2021-07-07-2</li><li>3.1.7 & 2021-07-09</li><li>3.1.8 & 2021-07-28</li><li>3.1.10 & 2021-07-28</li><li>3.1.11 & 2021-08-09</li><li>3.1.11 & 2021-08-24</li><li>3.1.11 & 2021-09-17</li><li>3.1.14 & 2021-09-28</li><li>3.1.14 & 2021-10-13</li><li>3.1.16 & 2021-10-18</li><li>3.1.16 & 2021-11-04</li><li>3.1.16 & 2021-11-09</li><li>3.1.16 & 2021-11-18</li><li>3.1.16 & 2021-11-25</li><li>3.1.17 & 2021-11-25</li><li>3.1.17 & 2021-12-06</li><li>3.1.17 & 2022-01-05</li><li>3.1.18 & 2022-01-20</li><li>3.1.19 & 2022-01-20</li><li>3.1.20 & 2022-02-02</li><li>3.1.20 & 2022-02-28</li></ul> Pangolin version & pangolin-data version <ul><li>4.0 & 1.2.133</li><li>4.0.1 & 1.2.133</li><li>4.0.2 & 1.2.133</li><li>4.0.3 & 1.2.133</li><li>4.0.4 & 1.2.133</li><li>4.0.5 & 1.3</li><li>4.0.6 & 1.6</li><li>4.0.6 & 1.8</li><li>4.0.6 & 1.9</li><li>4.1.1 & 1.11</li><li>4.1.2 & 1.12</li><li>4.1.2 & 1.13</li><li>4.1.2 & 1.14</li><li>4.1.3 & 1.15.1</li><li>4.1.3 & 1.16</li><li>4.1.3 & 1.17</li><li>4.2 & 1.18</li><li>4.2 & 1.18.1</li><li>4.2 & 1.18.1.1</li><li>4.2 & 1.19</li></ul> </details> Pangolin version & pangolin-data version <ul><li>4.3 & 1.20</li><li>4.3 & 1.21</li><li>4.3.1 & 1.22</li><li>4.3.1 & 1.23</li><li>4.3.1 & 1.23.1</li><li>4.3.1 & 1.23.1 with XDG_CACHE_HOME=/tmp</li><li>4.3.1 & 1.24</li><li>4.3.1 & 1.25.1</li><li>4.3.1 & 1.26</li><li>4.3.1 & 1.27</li><li>4.3.1 & 1.28</li><li>4.3.1 & 1.28.1</li><li>4.3.1 & 1.29</li><li>4.3.1 & 1.30</li><li>4.3.1 & 1.31</li></ul>https://github.com/cov-lineages/pangolin<br/>https://github.com/cov-lineages/pangoLEARN<br/>https://github.com/cov-lineages/pango-designation<br/>https://github.com/cov-lineages/scorpio<br/>https://github.com/cov-lineages/constellations<br/>https://github.com/cov-lineages/lineages (archived)<br/>https://github.com/hCoV-2019/pangolin (archived)
panqc <br/> docker pulls<ul><li>0.4.0</li></ul>https://github.com/maxgmarin/panqc/releases/tag/0.4.0
parallel-perl <br/> docker pulls<ul><li>20200722</li></ul>https://www.gnu.org/software/parallel
parsnp <br/> docker pulls<ul><li>1.5.6</li><li>2.0.4</li><li>2.0.5</li></ul>https://github.com/marbl/parsnp
pasty <br/> docker pulls<ul><li>1.0.2</li><li>1.0.3</li><li>2.2.1</li></ul>https://github.com/rpetit3/pasty
pbmm2 <br/> docker pulls<ul><li>1.13.1</li></ul>https://github.com/PacificBiosciences/pbmm2
Pavian <br/> docker pulls<ul><li>1.2.1</li></ul>https://github.com/fbreitwieser/pavian
pbptyper <br/> docker pulls<ul><li>1.0.0</li><li>1.0.1</li><li>1.0.4</li><li>2.0.0</li></ul>https://github.com/rpetit3/pbptyper
pbtk <br/> docker pulls<ul><li>3.1.1</li></ul>https://github.com/PacificBiosciences/pbtk
Phyml <br/> docker pulls<ul><li>3.3.20220408</li></ul>https://github.com/stephaneguindon/phyml
phyTreeViz <br/> docker pulls<ul><li>0.1.0</li><li>0.2.0</li></ul>https://github.com/moshi4/phyTreeViz/
Piggy <br/> docker pulls<ul><li>1.5</li></ul>https://github.com/harry-thorpe/piggy
Pilon <br/> docker pulls<ul><li>1.23.0</li><li>1.24</li></ul>https://github.com/broadinstitute/pilon
Piranha <br/> docker pulls<ul><li>1.0.4</li></ul>https://github.com/polio-nanopore/piranha
PlasmidFinder <br/> docker pulls<ul><li>2.1.6</li><li>2.1.6_2024-03-07</li></ul>https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/
PlasmidSeeker <br/> docker pulls<ul><li>1.0</li><li>1.3</li></ul>https://github.com/bioinfo-ut/PlasmidSeeker
pmga <br/> docker pulls<ul><li>3.0.2</li></ul>https://github.com/rpetit3/pmga
PolkaPox <br/> docker pulls<ul><li>1.0.0-beta</li></ul>https://github.com/CDCgov/polkapox
polypolish <br/> docker pulls<ul><li>0.5.0</li><li>0.6.0</li></ul>https://github.com/rrwick/Polypolish
PopPUNK <br/> docker pulls<ul><li>2.4.0</li><li>2.5.0</li><li>2.6.0</li><li>2.6.2</li><li>2.6.3</li><li>2.6.5</li></ul>https://github.com/bacpop/PopPUNK
Porechop <br/> docker pulls<ul><li>0.2.4</li></ul>https://github.com/rrwick/Porechop
PPanGGOLiN <br/> docker pulls<ul><li>1.2.105</li><li>2.0.3</li><li>2.0.5</li><li>2.1.2</li></ul>https://github.com/labgem/PPanGGOLiN
Prokka <br/> docker pulls<ul><li>1.13.4</li><li>1.14.0</li><li>1.14.5</li><li>1.14.6</li></ul>https://github.com/tseemann/prokka
pyCirclize <br/> docker pulls<ul><li>1.0.0</li><li>1.2.0</li><li>1.5.0</li><li>1.6.0</li><li>1.71</li></ul>https://github.com/moshi4/pyCirclize
pyGenomeViz <br/> docker pulls<ul><li>0.2.2</li><li>0.3.2</li><li>0.4.2</li><li>0.4.3</li><li>0.4.4</li><li>1.1.0</li></ul>https://github.com/moshi4/pyGenomeViz
pyMLST <br/> docker pulls<ul><li>2.1.5</li><li>2.1.6</li></ul>https://github.com/bvalot/pyMLST
pypolca <br/> docker pulls<ul><li>0.3.1</li></ul>https://github.com/gbouras13/pypolca
QUAST <br/> docker pulls<ul><li>5.0.0</li><li>5.0.2</li><li>5.2.0</li><li>5.2.0-slim</li><li>5.3.0</li><li>5.3.0-slim</li></ul>https://github.com/ablab/quast
QuickSNP <br/> docker pulls<ul><li>1.0.1</li></ul>https://github.com/k-florek/QuickSNP
racon <br/> docker pulls<ul><li>1.4.3</li><li>1.4.20</li><li>1.5.0</li></ul><li> https://github.com/lbcb-sci/racon </li><li> https://github.com/isovic/racon (ARCHIVED)</li>
rasusa <br/> docker pulls<ul><li>0.1.0</li><li>0.2.0</li><li>0.3.0</li><li>0.6.0</li><li>0.7.0</li><li>0.8.0</li><li>2.0.0</li><li>2.1.0</li></ul>https://github.com/mbhall88/rasusa
raven <br/> docker pulls<ul><li>1.5.1</li><li>1.8.1</li><li>1.8.3</li></ul>https://github.com/lbcb-sci/raven
RAxML <br/> docker pulls<ul><li>8.2.12</li><li>8.2.13</li></ul>https://github.com/stamatak/standard-RAxML
RAxML-NG <br/> docker pulls<ul><li>1.2.2</li></ul>https://github.com/amkozlov/raxml-ng
rdp <br/> docker pulls<ul><li>2.14</li></ul>https://sourceforge.net/projects/rdp-classifier/files/rdp-classifier/rdp_classifier_2.14.zip/download
ResFinder <br/> docker pulls<ul><li>4.1.1</li><li>4.5.0</li></ul>https://bitbucket.org/genomicepidemiology/resfinder/src/master/
Roary <br/> docker pulls<ul><li>3.12.0</li><li>3.13.0</li></ul>https://github.com/sanger-pathogens/Roary
SalmID <br/> docker pulls<ul><li>0.1.23</li></ul>https://github.com/hcdenbakker/SalmID
samclip <br/> docker pulls<ul><li>0.4.0</li></ul>https://github.com/tseemann/samclip
Samtools <br/> docker pulls<ul><li>1.9</li><li>1.10</li><li>1.11</li><li>1.12</li><li>1.13</li><li>1.14</li><li>1.15</li><li>1.16</li><li>1.16.1</li><li>1.17</li><li>1.17-2023-06</li><li>1.18</li><li>1.19</li><li>1.20</li><li>1.20.c</li></ul>https://github.com/samtools/samtools
SeqFu <br/> docker pulls<ul><li>1.20.3</li></ul>https://github.com/telatin/seqfu2
SeqKit <br/> docker pulls<ul><li>2.3.1</li><li>2.6.1</li><li>2.7.0</li><li>2.8.0</li><li>2.8.1</li><li>2.8.2</li></ul>https://github.com/shenwei356/seqkit
SeqSero <br/> docker pulls<ul><li>1.0.1</li></ul>https://github.com/denglab/SeqSero
SeqSero2 <br/> docker pulls<ul><li>0.1.0</li><li>1.0.0</li><li>1.0.2</li><li>1.1.0</li><li>1.1.1</li><li>1.2.1</li><li>1.3.1</li></ul>https://github.com/denglab/SeqSero2/
seqtk <br/> docker pulls<ul><li>1.3</li><li>1.4</li></ul>https://github.com/lh3/seqtk
seqyclean <br/> docker pulls<ul><li>1.10.09</li></ul>https://github.com/ibest/seqyclean
Seroba <br/> docker pulls<ul><li>1.0.0</li><li>1.0.2</li></ul>https://github.com/sanger-pathogens/seroba
SerotypeFinder <br/> docker pulls<ul><li>1.1 (perl version)</li><li>2.0.1 (python version)</li><li>2.0.2</ul>https://bitbucket.org/genomicepidemiology/serotypefinder/
ShigaPass <br/> docker pulls<ul><li>1.5.0</li></ul>https://github.com/imanyass/ShigaPass
shigatyper <br/> docker pulls<ul><li>2.0.1</li><li>2.0.2</li><li>2.0.3</li><li>2.0.4</li><li>2.0.5</li></ul>https://github.com/CFSAN-Biostatistics/shigatyper
ShigEiFinder <br/> docker pulls<ul><li>1.3.2</li><li>1.3.3</li><li>1.3.5</li></ul>https://github.com/LanLab/ShigEiFinder
Shovill <br/> docker pulls<ul><li>1.0.4</li><li>1.1.0</li></ul>https://github.com/tseemann/shovill
Shovill-se <br/> docker pulls<ul><li>1.1.0</li></ul>https://github.com/rpetit3/shovill/tree/v1.1.0se
SISTR <br/> docker pulls<ul><li>1.0.2</li><li>1.1.1</li></ul>https://github.com/phac-nml/sistr_cmd
SKA <br/> docker pulls<ul><li>1.0</li></ul>https://github.com/simonrharris/SKA
SKA2 <br/> docker pulls<ul><li>0.3.6</li><li>0.3.7</li><li>0.3.10</li></ul>https://github.com/bacpop/ska.rust
skani <br/> docker pulls<ul><li>0.2.0</li><li>0.2.1</li><li>0.2.2</li></ul>https://github.com/bluenote-1577/skani
SKESA <br/> docker pulls<ul><li>2.3.0</li><li>2.4.0 (gfa_connector & kmercounter included)</li><li>skesa.2.4.0_saute.1.3.0_2 (also known as 2.5.1)</li></ul>https://github.com/ncbi/SKESA
Smalt <br/> docker pulls<ul><li>0.7.6</li></ul>https://www.sanger.ac.uk/tool/smalt-0/
snpeff <br/> docker pulls<ul><li>5.1</li><li>5.2a</li></ul>https://pcingola.github.io/SnpEff
Snippy <br/> docker pulls<ul><li>4.4.5</li><li>4.5.1</li><li>4.6.0</li></ul>https://github.com/tseemann/snippy
snp-dists <br/> docker pulls<ul><li>0.6.2</li><li>0.8.2</li></ul>https://github.com/tseemann/snp-dists
SNP-sites <br/> docker pulls<ul><li>2.3.3</li><li>2.5.1</li></ul>https://github.com/sanger-pathogens/snp-sites
SNVPhyl-tools <br/> docker pulls<ul><li>1.8.2</li></ul>https://github.com/phac-nml/snvphyl-tools
SPAdes <br/> docker pulls<ul><li>3.8.2</li><li>3.12.0</li><li>3.13.0</li><li>3.14.0</li><li>3.14.1</li><li>3.15.0</li><li>3.15.1</li><li>3.15.2</li><li>3.15.3</li><li>3.15.4</li><li>3.15.5</li><li>4.0.0</li></ul>https://github.com/ablab/spades </br> http://cab.spbu.ru/software/spades/
SRA-toolkit <br/> docker pulls<ul><li>2.9.2</li><li>3.0.7</li></ul>https://github.com/ncbi/sra-tools
SRST2 <br/> docker pulls<ul><li>0.2.0</li><li>0.2.0 + custom Vibrio cholerae database</li></ul>https://github.com/katholt/srst2
Staramr <br/> docker pulls<ul><li>0.5.1</li><li>0.7.1</li><li>0.8.0</li><li>0.10.0</li></ul>https://github.com/phac-nml/staramr
stxtyper <br/> docker pulls<ul><li>1.0.24</li><li>1.0.27</li></ul>https://github.com/ncbi/stxtyper
sylph <br/> docker pulls<ul><li>0.4.1</li><li>0.5.1</li><li>0.6.0</li><li>0.6.1</li></ul>https://github.com/bluenote-1577/sylph
TBProfiler <br/> docker pulls<ul><li>4.3.0</li><li>4.4.0</li><li>4.4.2</li><li>5.0.1</li><li>6.2.0</li><li>6.2.1</li><li>6.3.0</li><li>6.4.0</li><li>6.4.1</li></ul>https://github.com/jodyphelan/TBProfiler
TipToft <br/> docker pulls<ul><li>1.0.0</li><li>1.0.2</li></ul>https://github.com/andrewjpage/tiptoft
Tostadas <br/> docker pulls<ul><li>0.2.0-beta</li><li>3.1.0</li><li>4.0.0</li></ul>https://github.com/CDCgov/tostadas
Treemmer <br/> docker pulls<ul><li>0.3</li></ul>https://git.scicore.unibas.ch/TBRU/Treemmer (archived, moved to GitHub) </br> https://github.com/fmenardo/Treemmer
Trimmomatic <br/> docker pulls<ul><li>0.38</li><li>0.39</li></ul>http://www.usadellab.org/cms/?page=trimmomatic </br>https://github.com/usadellab/Trimmomatic
Trycycler <br/> docker pulls<ul><li>0.3.1</li><li>0.3.2</li><li>0.3.3</li><li>0.5.0</li><li>0.5.3</li><li>0.5.4</li><li>0.5.5</li></ul>https://github.com/rrwick/Trycycler
Unicycler <br/> docker pulls<ul><li>0.4.7</li><li>0.4.8</li><li>0.4.9</li><li>0.5.0</li></ul>https://github.com/rrwick/Unicycler
VADR <br/> docker pulls<ul><li>1.1</li><li>1.1.2</li><li>1.1.3</li><li>1.2</li><li>1.2.1</li><li>1.3 & SARS-CoV-2 models 1.3-1</li><li>1.3 & SARS-CoV-2 models 1.3-2</li><li>1.4 & SARS-CoV-2 models 1.3-2</li><li>1.4.1 & SARS-CoV-2 models 1.3-2</li><li>1.4.2 & SARS-CoV-2 models 1.3-2, MPXV models 1.4.2-1</li><li>1.5 & SARS-CoV-2 models 1.3-2, MPXV models 1.4.2-1</li><li>1.5.1 & SARS-CoV-2 models 1.3-2, MPXV models 1.4.2-1, RSV models 1.5-2</li><li>1.6.3 & SARS-CoV-2 models 1.3-2, MPXV models 1.4.2-1, RSV models 1.5-2, Influenza v1.6.3-1</li><li>1.6.3 & SARS-CoV-2 models 1.3-2, MPXV models 1.4.2-1, RSV models 1.5-2, Influenza v1.6.3-1, HAV v1.0.0</li><li>1.6.3 & SARS-CoV-2 models 1.3-2, MPXV models 1.4.2-1, RSV models 1.5-2, Influenza v1.6.3-2, HAV v1.0.0</li></ul>https://github.com/nawrockie/vadr (archived, now redirects to ncbi/vadr) </br>https://github.com/ncbi/vadr
Verkko <br/> docker pulls<ul><li>2.0</li><li>2.1</li><li>2.2</li></ul>https://github.com/marbl/verkko
VIBRANT <br/> docker pulls<ul><li>1.2.1</li></ul>https://github.com/AnantharamanLab/VIBRANT
VIGOR4 <br/> docker pulls<ul><li>4.1.20190131</li><li>4.1.20200702</li></ul>https://github.com/JCVenterInstitute/VIGOR4
Viridian <br/> docker pulls<ul><li>1.2.2</li><li>1.3.0</li></ul>https://github.com/iqbal-lab-org/viridian
VirSorter2 <br/> docker pulls<ul><li>2.1</li></ul>https://github.com/jiarong/VirSorter2
VirulenceFinder <br/> docker pulls<ul><li>2.0.4</li><li>3.0.0</li></ul>https://bitbucket.org/genomicepidemiology/virulencefinder/src/master/ <br/> https://bitbucket.org/genomicepidemiology/virulencefinder_db/src/master/
wtdbg2 <br/> docker pulls<ul><li>2.5</li></ul>https://github.com/ruanjue/wtdbg2

You can also view the list of images on Docker hub here: https://hub.docker.com/r/staphb/

License

Authors/Maintainers

Each Dockerfile lists the author(s)/maintainer(s) as a metadata LABEL, but the authors/maintainers of the docker images are: