docker-builds

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.

This is a community resource, built and maintained 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

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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:

• Contributing
• Downloading Docker images
• Running Docker containers
• Developing Docker images
• Useful links

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

• Training materials (slides & exercises) from the North East Bioinformatics Regional Resource 2023 workshop Docker for Public Health Bioinformatics can be located here, within training/NE-BRR-docker-for-PH-bioinformatics-May2023/
• Video training from APHL 2024 workshop Intermediate Docker Bioinformatics Workshop can be located in APHL's e-learning resources

Logs

In December 2024, StaPH-B/docker-builds underwent a structural change where all Dockerfiles were placed in the subdirectory build-files.

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

Software	Version	Link
ABRicate	Click to see all versions 0.8.7 0.8.13 0.8.13s (+serotypefinder db) 0.9.8 1.0.0 1.0.1 (+ A. baumannii plasmid typing db) 1.0.1 (+ InsaFlu db) 1.0.1 (+ Vibrio cholerae db)	https://github.com/tseemann/abricate
ACI	Click to see all versions 1.4.20240116 1.15.250702	https://github.com/erinyoung/ACI
ANIclustermap	Click to see all versions 1.3.0 1.4.0 2.0.1	https://github.com/moshi4/ANIclustermap
any2fasta	Click to see all versions 0.4.2	https://github.com/tseemann/any2fasta
ARIBA	Click to see all versions 2.14.4 2.14.6 2.14.7	https://github.com/sanger-pathogens/ariba
artic	Click to see all versions 1.2.4-1.11.1 (artic-medaka) 1.2.4-1.12.0 (artic-medaka) 1.6.2 (Clair3) 1.7.5 1.8.0 1.8.4 1.8.5	https://github.com/artic-network/fieldbioinformatics
artic-ncov2019	Click to see all versions 1.3.0	https://github.com/artic-network/fieldbioinformatics
artic-ncov2019-epi2me	Click to see all versions 0.3.10	https://github.com/epi2me-labs/wf-artic
artic-ncov2019-medaka	Click to see all versions 1.1.0	https://github.com/artic-network/artic-ncov2019
artic-ncov2019-nanopolish	Click to see all versions 1.1.0	https://github.com/artic-network/artic-ncov2019
assembly_snptyper	Click to see all versions 0.1.1	https://github.com/boasvdp/assembly_snptyper
Augur	Click to see all versions 6.3.0 7.0.2 8.0.0 9.0.0 16.0.3 24.2.2 24.2.3 24.3.0 24.4.0 26.0.0 27.0.0 28.0.1 29.0.0 30.0.0 31.1.0 31.3.0 31.4.0 31.5.0 32.0.0	https://github.com/nextstrain/augur
Auspice	Click to see all versions 2.12.0	https://github.com/nextstrain/auspice
Autocycler	Click to see all versions 0.2.1 0.2.1-tutorial 0.4.0 0.4.0-tutorial	https://github.com/rrwick/Autocycler/
bakta	Click to see all versions 1.9.2 1.9.2-light 1.9.3 1.9.3-light 1.9.4 1.9.4-5.1-light 1.10.3 1.10.3-light 1.10.4 1.10.4-5.1-light 1.11.0 1.11.0-6.0-light 1.11.3 1.11.3-6.0-light 1.11.4 1.11.4-6.0-light	https://github.com/oschwengers/bakta
bandage	Click to see all versions 0.8.1	https://rrwick.github.io/Bandage/
BBTools	Click to see all versions 38.76 38.86 38.95 38.96 38.97 38.98 38.99 39.00 39.01 39.06 39.10 39.13 39.16 39.23 39.25 39.33 39.34 39.38	https://bbmap.org/
bcftools	Click to see all versions 1.10.2 1.11 1.12 1.13 1.14 1.15 1.16 1.17 1.18 1.19 1.20 1.20.c 1.21	https://github.com/samtools/bcftools
bedtools	Click to see all versions 2.29.2 2.30.0 2.31.0 2.31.1	https://bedtools.readthedocs.io/en/latest/ https://github.com/arq5x/bedtools2
berrywood-report-env	Click to see all versions 1.0	none
bindashtree	Click to see all versions 0.1.0 0.1.1	https://github.com/jianshu93/bindashtree
blast+	Click to see all versions 2.13.0 2.14.0 2.14.1 2.15.0 2.16.0 2.17.0	https://www.ncbi.nlm.nih.gov/books/NBK279690/
bowtie2	Click to see all versions 2.4.4 2.4.5 2.5.1 2.5.3 2.5.4	http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml https://github.com/BenLangmead/bowtie2
Bracken	Click to see all versions 2.9 3.1	https://ccb.jhu.edu/software/bracken/index.shtml?t=manual https://github.com/jenniferlu717/Bracken
BUSCO	Click to see all versions 5.4.7 5.6.1 5.6.1-prok-bacteria_odb10_2024-01-08 5.7.1 5.7.1-prok-bacteria_odb10_2024-01-08 5.8.0 5.8.0-prok-bacteria_odb10_2024-01-08 6.0.0 5.8.2-prok-bacteria_odb10_2024-11-14 5.8.2 6.0.0-prok-bacteria_odb12_2024-11-14</li	https://busco.ezlab.org/busco_userguide.html https://gitlab.com/ezlab/busco
BWA	Click to see all versions 0.7.17 0.7.18 0.7.19	https://github.com/lh3/bwa
Canu	Click to see all versions 2.0 2.1.1 2.2 2.3	https://canu.readthedocs.io/en/latest/ https://github.com/marbl/canu
Canu-Racon	Click to see all versions 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/
CAT	Click to see all versions 5.3 6.0.1	https://github.com/MGXlab/CAT_pack
cbird-util	Click to see all versions 2.0 2.1	https://github.com/Kincekara/C-BIRD
centroid	Click to see all versions 1.0.0	https://github.com/stjacqrm/centroid
CDC-SPN	Click to see all versions 0.1 (no version)	https://github.com/BenJamesMetcalf/Spn_Scripts_Reference
cfsan-snp-pipeline	Click to see all versions 2.0.2 2.2.1	https://github.com/CFSAN-Biostatistics/snp-pipeline
CheckM	Click to see all versions 1.2.2 1.2.3 1.2.4	https://github.com/Ecogenomics/CheckM
CheckM2	Click to see all versions 1.0.2 1.1.0	https://github.com/chklovski/CheckM2
CheckV	Click to see all versions 1.0.3	https://bitbucket.org/berkeleylab/checkv/
Circlator	Click to see all versions 1.5.6 1.5.5	https://github.com/sanger-pathogens/circlator
Circos	Click to see all versions 0.69-9	https://circos.ca/
CirculoCov	Click to see all versions 0.1.20240104	https://github.com/erinyoung/CirculoCov
Clair3	Click to see all versions 1.0.9 1.0.10 1.1.0 1.2.0	https://github.com/HKU-BAL/Clair3
Clustalo	Click to see all versions 1.2.4 1.2.4-2025	http://www.clustal.org/omega/
colorid	Click to see all versions 0.1.4.3 0.1.4.3	https://github.com/hcdenbakker/colorid
Core-SNP-filter	Click to see all versions 0.2.0	https://github.com/rrwick/Core-SNP-filter
cutshaw-report-env	Click to see all versions 1.0.0	https://github.com/VADGS/CutShaw
datasets-sars-cov-2	Click to see all versions 0.6.2 0.6.3 0.7.2	https://github.com/CDCgov/datasets-sars-cov-2
dnaapler	Click to see all versions 0.1.0 0.4.0 0.5.0 0.5.1 0.7.0 0.8.0 1.0.1 1.1.0 1.2.0 1.3.0	https://github.com/gbouras13/dnaapler
diamond	Click to see all versions 2.1.9 2.1.10 2.1.11 2.1.12 2.1.13	https://github.com/bbuchfink/diamond
dorado	Click to see all versions 0.8.0 0.8.3 0.9.0 0.9.0-cuda12.2.0-no_model 1.1.0-cuda12.2.0 1.1.0-cuda12.2.0-no_model	https://github.com/nanoporetech/dorado
dragonflye	Click to see all versions 1.0.14 1.1.1 1.1.2 1.2.0 1.2.1	https://github.com/rpetit3/dragonflye
Dr. PRG	Click to see all versions 0.1.1	https://mbh.sh/drprg/
DSK	Click to see all versions 0.0.100 2.3.3	https://gatb.inria.fr/software/dsk/
ectyper	Click to see all versions 2.0.0	https://github.com/phac-nml/ecoli_serotyping
el_gato	Click to see all versions 1.15.2 1.18.2 1.19.0 1.20.0 1.20.1 1.20.2 1.21.0 1.21.2 1.22.0	https://github.com/appliedbinf/el_gato https://github.com/CDCgov/el_gato
emboss	Click to see all versions 6.6.0 (no version) 6.4.0 (no version)	http://emboss.sourceforge.net
emmtyper	Click to see all versions 0.2.0 0.2.0-2412	https://github.com/MDU-PHL/emmtyper
emm-typing-tool	Click to see all versions 0.0.1 (no version)	https://github.com/phe-bioinformatics/emm-typing-tool
enaBrowserTools	Click to see all versions 1.7.1 1.7.2	https://github.com/enasequence/enaBrowserTools
EToKi	Click to see all versions 1.2.1	https://github.com/zheminzhou/EToKi
falco	Click to see all versions 1.2.5	https://github.com/smithlabcode/falco
FastANI	Click to see all versions 1.1 1.32 1.33 1.33 + RGDv2 1.34 1.34 + RGDv2	https://github.com/ParBLiSS/FastANI
fasten	Click to see all versions 0.7.2 0.8.1 0.8.5 0.8.7 0.9.0	https://github.com/lskatz/fasten
Fastp	Click to see all versions 0.23.2 0.23.4 0.24.0 0.24.1 1.0.1	http://opengene.org/fastp/ https://github.com/OpenGene/fastp
fastplong	Click to see all versions 0.2.2 0.4.1	https://github.com/OpenGene/fastplong
FastTree	Click to see all versions 2.1.11 2.2.0	http://www.microbesonline.org/fasttree/
FastQC	Click to see all versions 0.11.8 0.11.9 0.12.1	https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ https://github.com/s-andrews/FastQC
fastq-scan	Click to see all versions 0.4.3 0.4.4 1.0.0 1.0.1	https://github.com/rpetit3/fastq-scan
Freebayes	Click to see all versions 1.3.6 1.3.7 1.3.8 1.3.9 1.3.10	https://github.com/freebayes/freebayes
Filtlong	Click to see all versions 0.2.0 0.2.1 0.3.1	https://github.com/rrwick/filtlong
FLASH	Click to see all versions 1.2.11	http://ccb.jhu.edu/software/FLASH
Flye	Click to see all versions 2.5 2.7 2.8 2.9 2.9.1 2.9.2 2.9.3 2.9.4 2.9.5 2.9.6	https://github.com/fenderglass/Flye
Freyja	Click to see all versions 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 1.4.4 1.4.5 1.4.7 1.4.8 1.4.9 1.5.0 1.5.1 1.5.2 1.5.3 2.0.0 li>2.0.1	https://github.com/andersen-lab/Freyja
GAMBIT	Click to see all versions 0.3.0 0.4.0 0.5.0 1.0.0	https://github.com/jlumpe/gambit
GAMMA	Click to see all versions 1.4 2.1 2.2	https://github.com/rastanton/GAMMA/
GenoFLU	Click to see all versions 1.03 1.05 1.06	https://github.com/USDA-VS/GenoFLU
geNomad	Click to see all versions 1.7.4 1.8.0 1.8.1 1.11.0 1.11.1	https://github.com/apcamargo/genomad
GenoVi	Click to see all versions 0.2.16	https://github.com/robotoD/GenoVi
gfastats	Click to see all versions 1.3.6 1.3.7 1.3.10 1.3.11	https://github.com/vgl-hub/gfastats
grandeur_ref	Click to see all versions 4.5	Part of https://github.com/UPHL-BioNGS/Grandeur
Gubbins	Click to see all versions 3.3.3 3.3.4 3.3.5 3.4.1	https://github.com/nickjcroucher/gubbins
heatcluster	Click to see all versions 1.0.2c	https://github.com/DrB-S/heatcluster/tree/main
hmmer	Click to see all versions 3.3 3.3.2 3.4	http://hmmer.org/
hocort	Click to see all versions 1.2.2	https://github.com/ignasrum/hocort
homopolish	Click to see all versions 0.4.1	https://github.com/ythuang0522/homopolish/
hostile	Click to see all versions 1.1.0 2.0.0 2.0.1 2.0.2	https://github.com/bede/hostile
htslib	Click to see all versions 1.14 1.15 1.16 1.17 1.18 1.19 1.20 1.20.c 1.21 1.22.1	https://www.htslib.org/
igv-reports	Click to see all versions 1.12.0 1.15.1 1.16.0	https://github.com/igvteam/igv-reports
Integron Finder	Click to see all versions 2.0.5	https://github.com/gem-pasteur/Integron_Finder
iqtree	Click to see all versions 1.6.7	http://www.iqtree.org/
iqtree2	Click to see all versions 2.1.2 2.2.2.2 2.2.2.6 2.2.2.7 2.3.1 2.3.4 2.3.6 2.4.0	http://www.iqtree.org/
iqtree3	Click to see all versions 3.0.1	http://www.iqtree.org/
IPA	Click to see all versions 1.8.0	https://github.com/PacificBiosciences/pbipa
IRMA	Click to see all versions 1.0.2 1.0.3 1.1.2 1.1.3 1.1.4 1.2.0 1.3.0 1.3.1	https://wonder.cdc.gov/amd/flu/irma/ https://github.com/CDCgov/irma
isPcr	Click to see all versions 33	https://users.soe.ucsc.edu/~kent/
iVar	Click to see all versions 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 1.4.3 1.4.4 1.4.4-aligners (+bwa and minimap2)	https://github.com/andersen-lab/ivar
Jasmine	Click to see all versions 2.0.0 2.4.0	https://github.com/PacificBiosciences/jasmine
Kaptive	Click to see all versions 2.0.0 2.0.3 2.0.5 2.0.8 3.0.0b6 3.1.0	https://github.com/klebgenomics/Kaptive
Kleborate	Click to see all versions 2.0.4 2.1.0 2.2.0 2.3.2 2.3.2-2023-05 2.4.1 3.1.2 3.1.3 3.2.4	https://github.com/klebgenomics/Kleborate https://github.com/klebgenomics/Kaptive
kma	Click to see all versions 1.2.21 1.4.10 (no database) 1.4.14 (no database) 1.4.17 (no database) 1.5.2 (no database) 1.6.4 <	https://bitbucket.org/genomicepidemiology/kma/
Kraken	Click to see all versions 1.0 1.1.1 1.1.1 (no database)	https://github.com/DerrickWood/kraken
Kraken2	Click to see all versions 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) 2.1.3 2.1.4 2.1.5 2.1.6 2.1.6-viral	https://github.com/DerrickWood/kraken2
KrakenTools	Click to see all versions d4a2fbe	https://github.com/jenniferlu717/KrakenTools
KrakenUniq	Click to see all versions 1.0.4 (no database)	https://github.com/fbreitwieser/krakenuniq
krocus	Click to see all versions 1.0.3	https://github.com/andrewjpage/krocus/
Krona	Click to see all versions 2.8.1	https://github.com/marbl/Krona
kSNP3	Click to see all versions 3.1	https://sourceforge.net/projects/ksnp/
kSNP4	Click to see all versions 4.0 4.1	https://sourceforge.net/projects/ksnp/
label	Click to see all versions 0.6.4 0.7.1 0.7.2	https://wonder.cdc.gov/amd/flu/label
legsta	Click to see all versions 0.3.7 0.5.1	https://github.com/tseemann/legsta
liftoff	Click to see all versions 1.6.3	https://github.com/agshumate/Liftoff
lima	Click to see all versions 2.9.0 2.9.0-Rscripts 2.12.0 2.12.0-Rscripts 2.13.0 2.13.0-Rscripts	https://github.com/PacificBiosciences/barcoding
longshot	Click to see all versions 0.4.5 1.0.0	https://github.com/pjedge/longshot
lrge	Click to see all versions 0.1.3 0.2.0	https://github.com/mbhall88/lrge
Lyve-SET (includes CG-Pipeline scripts and raxml)	Click to see all versions 1.1.4f 2.0.1	https://github.com/lskatz/lyve-SET https://github.com/lskatz/CG-Pipeline
MAFFT	Click to see all versions 7.450 7.475 7.505 7.520 7.526	https://mafft.cbrc.jp/alignment/software/
Mash	Click to see all versions 2.1 2.2 2.3 2.3-CBIRDv2	https://github.com/marbl/Mash
mashtree	Click to see all versions 0.52.0 0.57.0 1.0.4 1.2.0 1.4.6	https://github.com/lskatz/mashtree
MaSuRCA	Click to see all versions 4.0.8 4.0.9 4.1.0	https://github.com/alekseyzimin/masurca
medaka	Click to see all versions 0.8.1 1.0.1 1.2.0 2.0.0 2.0.1 2.1.0 2.1.1	https://github.com/nanoporetech/medaka
meningotype	Click to see all versions 0.8.5	https://github.com/MDU-PHL/meningotype
metaphlan	Click to see all versions 3.0.3-no-db (no database) 3.0.3 (~3GB db) 4.1.0 (no database) 4.1.1 (no database) 4.2.2 4.2.4	https://github.com/biobakery/MetaPhlAn
MIDAS	Click to see all versions 1.3.2 (no database)	https://github.com/snayfach/MIDAS
minimap2	Click to see all versions 2.17 2.18 2.21 2.22 2.23 2.24 2.25 2.26 2.27 2.28 2.29 2.30	https://github.com/lh3/minimap2
minipolish	Click to see all versions 0.1.3 0.2.0	https://github.com/rrwick/Minipolish
mlst	Click to see all versions 2.16.2 2.17.6 2.19.0 2.22.0 2.22.1 2.23.0 2.23.0-2023-07 2.23.0-2023-08 2.23.0-2024-01 2.23.0-2024-03 2.23.0-2024-12-31	https://github.com/tseemann/mlst
MMseqs2	Click to see all versions 17-b804f 18-8cc5c	https://github.com/soedinglab/MMseqs2
mob-suite	Click to see all versions 3.1.9	https://github.com/phac-nml/mob-suite
Mugsy	Click to see all versions 1r2.3	http://mugsy.sourceforge.net/
MultiQC	Click to see all versions 1.7 1.8 1.18 1.19 1.22.2 1.22.3 1.25 1.26 1.27.1 1.28 1.30 1.31	https://github.com/MultiQC/MultiQC
Mummer	Click to see all versions 4.0.0 4.0.0 + RGDv2 4.0.0 + RGDv2 + gnuplot 4.0.1	https://github.com/mummer4/mummer
Mykrobe + Genotyphi + sonneityping	Click to see all versions 0.11.0 (Mykrobe) & 1.9.1 (Genotyphi) 0.12.1 (Mykrobe) & 1.9.1 (Genotyphi) & 7d18a7c (sonneityping) 0.12.1 (Mykrobe) & 2.0 (Genotyphi) & v20210201 (sonneityping) 0.12.2 (Mykrobe) & 2.0 (Genotyphi) & v20210201 (sonneityping) 0.13.0	https://github.com/Mykrobe-tools/mykrobe https://github.com/typhoidgenomics/genotyphi https://github.com/katholt/sonneityping
myloasm	Click to see all versions 0.1.0 0.2.0	https://github.com/bluenote-1577/myloasm
NanoPlot	Click to see all versions 1.27.0 1.29.0 1.30.1 1.32.0 1.33.0 1.40.0 1.41.6 1.42.0	https://github.com/wdecoster/NanoPlot
ngmaster	Click to see all versions 0.5.8 1.0.0	https://github.com/MDU-PHL/ngmaster
NCBI Datasets	Click to see all versions 13.31.0 13.35.0 13.43.2 14.0.0 14.3.0 14.7.0 14.13.2 14.20.0 14.27.0 15.1.0 15.2.0 15.11.0 15.27.1 15.31.0 16.2.0 16.8.1 16.10.3 16.15.0 16.22.1 16.30.0 16.35.0 16.38.1 16.41.0 18.0.2 18.5.0 18.7.0 18.9.0	https://github.com/ncbi/datasets https://www.ncbi.nlm.nih.gov/datasets/docs/v2/
NCBI AMRFinderPlus	Click to see all 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 3.11.14 & 2023-04-17.1 3.11.17 & 2023-07-13.2 3.11.18 & 2023-08-08.2 3.11.20 & 2023-09-26.1 3.11.26 & 2023-11-15.1 3.12.8 & 2024-01-31.1 3.12.8 & 2024-05-02.2 3.12.8 & 2024-07-22.1 4.0.3 & 2024-10-22.1 (stxtyper now included) 4.0.3 & 2024-12-18.1 4.0.15 & 2024-12-18.1 4.0.19 & 2024-12-18.1 4.0.22 & 2025-03-25.1 4.0.23-2025-06-03.1 4.0.23-2025-07-16.1	https://github.com/ncbi/amr
NCBI table2asn	Click to see all versions 1.26.678 1.28.943 1.28.1021 1.28.1094 1.29.1151	https://www.ncbi.nlm.nih.gov/genbank/table2asn/ https://ftp.ncbi.nlm.nih.gov/asn1-converters/versions/2022-06-14/by_program/table2asn/
ONTime	Click to see all versions 0.2.3 0.3.1	https://github.com/mbhall88/ontime
OrthoFinder	Click to see all versions 2.17 2.5.5 3.0.1b1	https://github.com/davidemms/OrthoFinder
Panaroo	Click to see all versions 1.2.10 1.3.4 1.5.0 1.5.1 1.5.2	https://github.com/gtonkinhill/panaroo
pandas	Click to see all versions 2.2.3 2.3.0 2.3.2 2.3.3	https://github.com/pandas-dev/pandas
pango_aliasor	Click to see all versions 0.3.0	https://github.com/corneliusroemer/pango_aliasor
Pangolin	Click to see all 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 4.3 & 1.21 4.3.1 & 1.22 4.3.1 & 1.23 4.3.1 & 1.23.1 4.3.1 & 1.23.1 with XDG_CACHE_HOME=/tmp 4.3.1 & 1.24 4.3.1 & 1.25.1 4.3.1 & 1.26 4.3.1 & 1.27 4.3.1 & 1.28 4.3.1 & 1.28.1 4.3.1 & 1.29 4.3.1 & 1.30 4.3.1 & 1.31 4.3.1 & 1.32 4.3.1 & 1.33 4.3.1 & 1.34 4.3.1 & 1.35	https://github.com/cov-lineages/pangolin https://github.com/cov-lineages/pangolin-data 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)
panqc	Click to see all versions 0.4.0	https://github.com/maxgmarin/panqc/releases/tag/0.4.0
parallel-perl	Click to see all versions 20200722	https://www.gnu.org/software/parallel
parsnp	Click to see all versions 1.5.6 2.0.4 2.0.5 2.1.2 2.1.4	https://github.com/marbl/parsnp
pasty	Click to see all versions 1.0.2 1.0.3 2.2.1	https://github.com/rpetit3/pasty
Pavian	Click to see all versions 1.2.1	https://github.com/fbreitwieser/pavian
pbmm2	Click to see all versions 1.13.1 1.16.0 1.17.0	https://github.com/PacificBiosciences/pbmm2
pbptyper	Click to see all versions 1.0.0 1.0.1 1.0.4 2.0.0	https://github.com/rpetit3/pbptyper
pbtk	Click to see all versions 3.1.1 3.4.0 3.5.0	https://github.com/PacificBiosciences/pbtk
Phyml	Click to see all versions 3.3.20220408 3.3.20250506 3.3.20250515	https://github.com/stephaneguindon/phyml
phyTreeViz	Click to see all versions 0.1.0 0.2.0	https://github.com/moshi4/phyTreeViz/
Piggy	Click to see all versions 1.5	https://github.com/harry-thorpe/piggy
Pilon	Click to see all versions 1.23.0 1.24	https://github.com/broadinstitute/pilon
Piranha	Click to see all versions 1.0.4 1.4.2 1.5.3	https://github.com/polio-nanopore/piranha
PlasmidFinder	Click to see all versions 2.1.6 2.1.6_2024-03-07 2.1.6_2025-02-19 3.0.1	https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/
PlasmidSeeker	Click to see all versions 1.0 1.3	https://github.com/bioinfo-ut/PlasmidSeeker
plassembler	Click to see all versions 1.6.2 1.8.0	https://github.com/gbouras13/plassembler
pling	Click to see all versions 2.0.0 2.0.1	https://github.com/iqbal-lab-org/pling
pmga	Click to see all versions 3.0.2	https://github.com/rpetit3/pmga
pod5	Click to see all versions 0.3.23 0.3.27	https://github.com/nanoporetech/pod5-file-format
PolkaPox	Click to see all versions 1.0.0-beta	https://github.com/CDCgov/polkapox
polypolish	Click to see all versions 0.5.0 0.6.0 0.6.0-bwa 0.6.1	https://github.com/rrwick/Polypolish
PopPUNK	Click to see all versions 2.4.0 2.5.0 2.6.0 2.6.2 2.6.3 2.6.5 2.7.5 2.7.6	https://github.com/bacpop/PopPUNK
Porechop	Click to see all versions 0.2.4	https://github.com/rrwick/Porechop
PPanGGOLiN	Click to see all versions 1.2.105 2.0.3 2.0.5 2.1.2 2.2.1 2.2.4 2.2.5	https://github.com/labgem/PPanGGOLiN
Primer3	Click to see all versions 2.3.4 2.6.1	https://github.com/primer3-org/primer3
Prokka	Click to see all versions 1.13.4 1.14.0 1.14.5 1.14.6	https://github.com/tseemann/prokka
pyCirclize	Click to see all versions 1.0.0 1.2.0 1.5.0 1.6.0 1.7.1 1.7.2 1.9.0 1.9.1 1.10.0	https://github.com/moshi4/pyCirclize
pyGenomeViz	Click to see all versions 0.2.2 0.3.2 0.4.2 0.4.3 0.4.4 1.1.0 1.5.0 1.6.1	https://github.com/moshi4/pyGenomeViz
pyMLST	Click to see all versions 2.1.5 2.1.6 2.2.2	https://github.com/bvalot/pyMLST
pypolca	Click to see all versions 0.3.1 0.4.0	https://github.com/gbouras13/pypolca
QualiMap	Click to see all versions 2.3	http://qualimap.conesalab.org/
QUAST	Click to see all versions 5.0.0 5.0.2 5.2.0 5.2.0-slim 5.3.0 5.3.0-slim	https://github.com/ablab/quast
QuickSNP	Click to see all versions 1.0.1	https://github.com/k-florek/QuickSNP
racon	Click to see all versions 1.4.3 1.4.20 1.5.0 1.5.0-minimap2	https://github.com/lbcb-sci/racon https://github.com/isovic/racon (ARCHIVED)
rasusa	Click to see all versions 0.1.0 0.2.0 0.3.0 0.6.0 0.7.0 0.8.0 2.0.0 2.1.0 2.2.2	https://github.com/mbhall88/rasusa
raven	Click to see all versions 1.5.1 1.8.1 1.8.3	https://github.com/lbcb-sci/raven
RAxML	Click to see all versions 8.2.12 8.2.13	https://github.com/stamatak/standard-RAxML
RAxML-NG	Click to see all versions 1.2.2	https://github.com/amkozlov/raxml-ng
rdp	Click to see all versions 2.14	https://sourceforge.net/projects/rdp-classifier/files/rdp-classifier/rdp_classifier_2.14.zip/download
ResFinder	Click to see all versions 4.1.1 4.5.0 4.6.0 4.7.2	https://bitbucket.org/genomicepidemiology/resfinder/src/master/ https://bitbucket.org/genomicepidemiology/resfinder_db/src/master/ https://bitbucket.org/genomicepidemiology/pointfinder_db/ https://bitbucket.org/genomicepidemiology/disinfinder_db/
Roary	Click to see all versions 3.12.0 3.13.0	https://github.com/sanger-pathogens/Roary
SalmID	Click to see all versions 0.1.23	https://github.com/hcdenbakker/SalmID
samclip	Click to see all versions 0.4.0	https://github.com/tseemann/samclip
Samtools	Click to see all versions 1.9 1.10 1.11 1.12 1.13 1.14 1.15 1.16 1.16.1 1.17 1.17-2023-06 1.18 1.19 1.20 1.20.c 1.21 1.22 1.22.1	https://github.com/samtools/samtools
SeqFu	Click to see all versions 1.20.3 1.22.3	https://github.com/telatin/seqfu2
SeqKit	Click to see all versions 2.3.1 2.6.1 2.7.0 2.8.0 2.8.1 2.8.2 2.9.0 2.10.0 2.10.1	https://github.com/shenwei356/seqkit
SeqSender	Click to see all versions 1.3.3 1.3.4	https://github.com/CDCgov/seqsender
SeqSero	Click to see all versions 1.0.1	https://github.com/denglab/SeqSero
SeqSero2	Click to see all versions 0.1.0 1.0.0 1.0.2 1.1.0 1.1.1 1.2.1 1.3.1 1.3.1-micromamba	https://github.com/denglab/SeqSero2/
SeqSero2S	Click to see all versions 1.1.4	https://github.com/LSTUGA/SeqSero2S/
seqtk	Click to see all versions 1.3 1.4 1.5	https://github.com/lh3/seqtk
seqyclean	Click to see all versions 1.10.09	https://github.com/ibest/seqyclean
Seroba	Click to see all versions 1.0.0 1.0.2 2.0.5	https://github.com/sanger-pathogens/seroba https://github.com/GlobalPneumoSeq/seroba
SerotypeFinder	Click to see all versions 1.1 (perl version) 2.0.1 (python version) 2.0.2	https://bitbucket.org/genomicepidemiology/serotypefinder/
ShigaPass	Click to see all versions 1.5.0	https://github.com/imanyass/ShigaPass
shigatyper	Click to see all versions 2.0.1 2.0.2 2.0.3 2.0.4 2.0.5	https://github.com/CFSAN-Biostatistics/shigatyper
ShigEiFinder	Click to see all versions 1.3.2 1.3.3 1.3.5	https://github.com/LanLab/ShigEiFinder
Shovill	Click to see all versions 1.0.4 1.1.0	https://github.com/tseemann/shovill
Shovill-se	Click to see all versions 1.1.0	https://github.com/rpetit3/shovill/tree/v1.1.0se
SISTR	Click to see all versions 1.0.2 1.1.1 1.1.2 1.1.3	https://github.com/phac-nml/sistr_cmd
SKA	Click to see all versions 1.0	https://github.com/simonrharris/SKA
SKA2	Click to see all versions 0.3.6 0.3.7 0.3.10 0.4.0 0.4.1	https://github.com/bacpop/ska.rust
skani	Click to see all versions 0.2.0 0.2.1 0.2.2 0.3.0 0.3.1	https://github.com/bluenote-1577/skani
SKESA	Click to see all versions 2.3.0 2.4.0 (gfa_connector & kmercounter included) skesa.2.4.0_saute.1.3.0_2 (also known as 2.5.1)	https://github.com/ncbi/SKESA
Smalt	Click to see all versions 0.7.6	https://www.sanger.ac.uk/tool/smalt-0/
snpeff	Click to see all versions 5.1 5.2a 5.2f	https://pcingola.github.io/SnpEff
Snippy	Click to see all versions 4.4.5 4.5.1 4.6.0	https://github.com/tseemann/snippy
snp-dists	Click to see all versions 0.6.2 0.8.2	https://github.com/tseemann/snp-dists
SNP-sites	Click to see all versions 2.3.3 2.5.1	https://github.com/sanger-pathogens/snp-sites
SNVPhyl-tools	Click to see all versions 1.8.2	https://github.com/phac-nml/snvphyl-tools
SPAdes	Click to see all versions 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 4.0.0 4.1.0 4.2.0	https://github.com/ablab/spades http://cab.spbu.ru/software/spades/
SRA-toolkit	Click to see all versions 2.9.2 3.0.7 3.2.0 3.2.1	https://github.com/ncbi/sra-tools
SRST2	Click to see all versions 0.2.0 0.2.0 + custom Vibrio cholerae database	https://github.com/katholt/srst2
Staramr	Click to see all versions 0.5.1 0.7.1 0.8.0 0.10.0 0.11.0 0.11.1	https://github.com/phac-nml/staramr
stxtyper	Click to see all versions 1.0.24 1.0.27 1.0.31 1.0.40 1.0.42	https://github.com/ncbi/stxtyper
sylph	Click to see all versions 0.4.1 0.5.1 0.6.0 0.6.1 0.8.0 0.8.1 0.9.0	https://github.com/bluenote-1577/sylph
TBProfiler	Click to see all versions 4.3.0 4.4.0 4.4.2 5.0.1 6.2.0 6.2.1 6.3.0 6.4.0 6.4.1 6.6.2 6.6.3 6.6.5	https://github.com/jodyphelan/TBProfiler https://github.com/jodyphelan/tbdb
TipToft	Click to see all versions 1.0.0 1.0.2	https://github.com/andrewjpage/tiptoft
Tostadas	Click to see all versions 0.2.0-beta 3.1.0 4.0.0	https://github.com/CDCgov/tostadas
toulligQC	Click to see all versions 2.7.1	https://github.com/GenomiqueENS/toulligQC
transcluster	Click to see all versions 77f4909	https://github.com/JamesStimson/transcluster
Treemmer	Click to see all versions 0.3	https://git.scicore.unibas.ch/TBRU/Treemmer (archived, moved to GitHub) https://github.com/fmenardo/Treemmer
trimal	Click to see all versions 1.2 1.5.0	https://github.com/inab/trimal
Trimmomatic	Click to see all versions 0.38 0.39 0.40	http://www.usadellab.org/cms/?page=trimmomatic https://github.com/usadellab/Trimmomatic
Trycycler	Click to see all versions 0.3.1 0.3.2 0.3.3 0.5.0 0.5.3 0.5.4 0.5.5 0.5.6	https://github.com/rrwick/Trycycler
Unicycler	Click to see all versions 0.4.7 0.4.8 0.4.9 0.5.0 0.5.1	https://github.com/rrwick/Unicycler
UShER	Click to see all versions 0.6.3 0.6.6	https://github.com/yatisht/usher
VADR	Click to see all versions 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 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 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 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 1.6.4 1.6.4-flu 1.6.4-hav 1.6.4-mev 1.6.4-mpxv 1.6.4-rsv 1.6.4-sarscov2 1.6.4-2505 which includes models for flu, rsv, mpxv, and sarscov2 1.7	https://github.com/nawrockie/vadr (archived, now redirects to ncbi/vadr) https://github.com/ncbi/vadr
Verkko	Click to see all versions 2.0 2.1 2.2 2.2.1	https://github.com/marbl/verkko
VIBRANT	Click to see all versions 1.2.1	https://github.com/AnantharamanLab/VIBRANT
VIGOR4	Click to see all versions 4.1.20190131 4.1.20200702	https://github.com/JCVenterInstitute/VIGOR4
Viridian	Click to see all versions 1.2.2 1.3.0 1.4.0 1.5.1	https://github.com/iqbal-lab-org/viridian
VirSorter2	Click to see all versions 2.1 2.2.4	https://github.com/jiarong/VirSorter2
VirulenceFinder	Click to see all versions 2.0.4 3.0.0 3.1.0 3.2.0	https://bitbucket.org/genomicepidemiology/virulencefinder/src/master/ https://bitbucket.org/genomicepidemiology/virulencefinder_db/src/master/
wtdbg2	Click to see all versions 2.5	https://github.com/ruanjue/wtdbg2

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

License

• GNU GPLv3 license was added 2020-01-16
• We keep a list of the licenses for the main software within the docker images here: Program_Licenses.md
• Links to licenses for each program should also be listed as a metadata LABEL within each dockerfile

Citation

If you have found this resource useful please use the following citation in addition to the citations of the tools being used:

Florek, K. R., Young, E. L., Incekara, K., Libuit, K. G., & Kapsak, C. J. (2025). Advantages of Software Containerization in Public Health Infectious Disease Genomic Surveillance. Emerging Infectious Diseases, 31(13, Supplement), S18–S21. https://doi.org/10.3201/eid3113.241363

APA & BibTeX formatted citations are available via the CITATION.cff file. Click on the button "Cite this repository" at the top of this page to view.

Hypothetical text example:

Reads were assembled with spades version 4.2.0 (PMID: 32559359) before AMR gene identification with AMRFinder version 4.0.23 database version 2025-06-03.1 (PMID: 34135355) using StaPH-B/docker-builds docker images (PMID: 40359055)