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Gitpod ready-to-code

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
Loading

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.

Software Version Link
ABRicate
docker pulls
https://github.com/tseemann/abricate
ACI
docker pulls
https://github.com/erinyoung/ACI
ANIclustermap
docker pulls
https://github.com/moshi4/ANIclustermap
any2fasta
docker pulls
  • 0.4.2
https://github.com/tseemann/any2fasta
ARIBA
docker pulls
https://github.com/sanger-pathogens/ariba
artic
docker pulls
https://github.com/artic-network/fieldbioinformatics
artic-ncov2019
docker pulls
  • 1.3.0
https://github.com/artic-network/fieldbioinformatics
artic-ncov2019-epi2me
docker pulls
  • 0.3.10
https://github.com/epi2me-labs/wf-artic
artic-ncov2019-medaka
docker pulls
  • 1.1.0
https://github.com/artic-network/artic-ncov2019
artic-ncov2019-nanopolish
docker pulls
  • 1.1.0
https://github.com/artic-network/artic-ncov2019
assembly_snptyper
docker pulls
https://github.com/boasvdp/assembly_snptyper
Augur
docker pulls
https://github.com/nextstrain/augur
Auspice
docker pulls
  • 2.12.0
https://github.com/nextstrain/auspice
bakta
docker pulls
https://github.com/oschwengers/bakta
bandage
docker pulls
https://rrwick.github.io/Bandage/
BBTools
docker pulls
https://jgi.doe.gov/data-and-tools/bbtools/
bcftools
docker pulls
https://github.com/samtools/bcftools
bedtools
docker pulls
https://bedtools.readthedocs.io/en/latest/
https://github.com/arq5x/bedtools2
berrywood-report-env
docker pulls
  • 1.0
none
blast+
docker pulls
https://www.ncbi.nlm.nih.gov/books/NBK279690/
bowtie2
docker pulls
http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
https://github.com/BenLangmead/bowtie2
Bracken
docker pulls
https://ccb.jhu.edu/software/bracken/index.shtml?t=manual
https://github.com/jenniferlu717/Bracken
BUSCO
docker pulls
https://busco.ezlab.org/busco_userguide.html
https://gitlab.com/ezlab/busco
BWA
docker pulls
https://github.com/lh3/bwa
Canu
docker pulls
  • 2.0
  • 2.1.1
  • 2.2
https://canu.readthedocs.io/en/latest/
https://github.com/marbl/canu
Canu-Racon
docker pulls
  • 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
docker pulls
  • 1.0.0
https://github.com/stjacqrm/centroid
CDC-SPN
docker pulls
  • 0.1 (no version)
https://github.com/BenJamesMetcalf/Spn_Scripts_Reference
cfsan-snp-pipeline
docker pulls
  • 2.0.2
  • 2.2.1
https://github.com/CFSAN-Biostatistics/snp-pipeline
CheckM
docker pulls
https://github.com/Ecogenomics/CheckM
CheckV
docker pulls
https://bitbucket.org/berkeleylab/checkv/
Circlator
docker pulls
  • 1.5.6
  • 1.5.5
https://github.com/sanger-pathogens/circlator
Circos
docker pulls
https://circos.ca/
CirculoCov
docker pulls
https://github.com/erinyoung/CirculoCov
Clair3
docker pulls
https://github.com/HKU-BAL/Clair3
Clustalo
docker pulls
  • 1.2.4
http://www.clustal.org/omega/
colorid
docker pulls
  • 0.1.4.3
https://github.com/hcdenbakker/colorid
cutshaw-report-env
docker pulls
  • 1.0.0
https://github.com/VADGS/CutShaw
datasets-sars-cov-2
docker pulls
  • 0.6.2
  • 0.6.3
  • 0.7.2
https://github.com/CDCgov/datasets-sars-cov-2
diamond
docker pulls
https://github.com/bbuchfink/diamond
dnaapler
docker pulls
https://github.com/gbouras13/dnaapler
dorado
docker pulls
https://github.com/nanoporetech/dorado
dragonflye
docker pulls
https://github.com/rpetit3/dragonflye
Dr. PRG
docker pulls
https://mbh.sh/drprg/
DSK
docker pulls
https://gatb.inria.fr/software/dsk/
el_gato
docker pulls
https://github.com/appliedbinf/el_gato
emboss
docker pulls
  • 6.6.0 (no version)
http://emboss.sourceforge.net
emmtyper
docker pulls
  • 0.2.0
https://github.com/MDU-PHL/emmtyper
emm-typing-tool
docker pulls
  • 0.0.1 (no version)
https://github.com/phe-bioinformatics/emm-typing-tool
EToKi
docker pulls
  • 1.2.1
https://github.com/zheminzhou/EToKi
FastANI
docker pulls
https://github.com/ParBLiSS/FastANI
fasten
docker pulls
https://github.com/lskatz/fasten
Fastp
docker pulls
http://opengene.org/fastp/
https://github.com/OpenGene/fastp
FastTree
docker pulls
  • 2.1.11
http://www.microbesonline.org/fasttree/
FastQC
docker pulls
  • 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
docker pulls
  • 0.4.3
  • 0.4.4
  • 1.0.0
  • 1.0.1
https://github.com/rpetit3/fastq-scan
Freebayes
docker pulls
  • 1.3.6
  • 1.3.7
  • 1.3.7
  • 1.3.7
https://github.com/freebayes/freebayes
Filtlong
docker pulls
  • 0.2.0
  • 0.2.1
https://github.com/rrwick/filtlong
FLASH
docker pulls
  • 1.2.11
http://ccb.jhu.edu/software/FLASH
Flye
docker pulls
https://github.com/fenderglass/Flye
Freyja
docker pulls
https://github.com/andersen-lab/Freyja
GAMBIT
docker pulls
  • 0.3.0
  • 0.4.0
  • 0.5.0
  • 1.0.0
https://github.com/jlumpe/gambit
GAMMA
docker pulls
  • 1.4
  • 2.1
  • 2.2
https://github.com/rastanton/GAMMA/
GenoFLU
docker pulls
https://github.com/USDA-VS/GenoFLU
geNomad
docker pulls
https://github.com/apcamargo/genomad
GenoVi
docker pulls
https://github.com/robotoD/GenoVi
gfastats
docker pulls
https://github.com/vgl-hub/gfastats
Gubbins
docker pulls
https://github.com/nickjcroucher/gubbins
heatcluster
docker pulls
https://github.com/DrB-S/heatcluster/tree/main
hmmer
docker pulls
http://hmmer.org/
homopolish
docker pulls
  • 0.4.1
https://github.com/ythuang0522/homopolish/
htslib
docker pulls
https://www.htslib.org/
Integron Finder
docker pulls
https://github.com/gem-pasteur/Integron_Finder
iqtree
docker pulls
  • 1.6.7
http://www.iqtree.org/
iqtree2
docker pulls
http://www.iqtree.org/
IPA
docker pulls
https://github.com/PacificBiosciences/pbipa
IRMA
docker pulls
  • 1.0.2
  • 1.0.3
  • 1.1.2
  • 1.1.3
  • 1.1.4
https://wonder.cdc.gov/amd/flu/irma/
isPcr
docker pulls
https://users.soe.ucsc.edu/~kent/
iVar
docker pulls
https://github.com/andersen-lab/ivar
Jasmine
docker pulls
https://github.com/PacificBiosciences/jasmine
Kaptive
docker pulls
https://github.com/klebgenomics/Kaptive
Kleborate
docker pulls
https://github.com/katholt/Kleborate/
https://github.com/katholt/Kaptive/
kma
docker pulls
  • 1.2.21
  • 1.4.10 (no database)
  • 1.4.14 (no database)
https://bitbucket.org/genomicepidemiology/kma/
Kraken
docker pulls
  • 1.0
  • 1.1.1
  • 1.1.1 (no database)
https://github.com/DerrickWood/kraken
Kraken2
docker pulls
  • 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 (no db)
https://github.com/DerrickWood/kraken2
KrakenUniq
docker pulls
https://github.com/fbreitwieser/krakenuniq
kSNP3
docker pulls
  • 3.1
https://sourceforge.net/projects/ksnp/
kSNP4
docker pulls
https://sourceforge.net/projects/ksnp/
label
docker pulls
https://wonder.cdc.gov/amd/flu/label
legsta
docker pulls
  • 0.3.7
  • 0.5.1
https://github.com/tseemann/legsta
liftoff
docker pulls
  • 1.6.3
https://github.com/agshumate/Liftoff
lima
docker pulls
https://github.com/PacificBiosciences/barcoding
longshot
docker pulls
https://github.com/pjedge/longshot
Lyve-SET (includes CG-Pipeline scripts and raxml)
docker pulls
  • 1.1.4f
  • 2.0.1
https://github.com/lskatz/lyve-SET https://github.com/lskatz/CG-Pipeline
MAFFT
docker pulls
https://mafft.cbrc.jp/alignment/software/
Mash
docker pulls
  • 2.1
  • 2.2
  • 2.3
https://github.com/marbl/Mash
mashtree
docker pulls
https://github.com/lskatz/mashtree
MaSuRCA
docker pulls
  • 4.0.8
  • 4.0.9
  • 4.1.0
https://github.com/alekseyzimin/masurca
medaka
docker pulls
https://github.com/nanoporetech/medaka
metaphlan
docker pulls
https://github.com/biobakery/MetaPhlAn
MIDAS
docker pulls
  • 1.3.2 (no database)
https://github.com/snayfach/MIDAS
minimap2
docker pulls
https://github.com/lh3/minimap2
minipolish
docker pulls
  • 0.1.3
https://github.com/rrwick/Minipolish
mlst
docker pulls
https://github.com/tseemann/mlst
Mugsy
docker pulls
  • 1r2.3
http://mugsy.sourceforge.net/
MultiQC
docker pulls
https://github.com/MultiQC/MultiQC
Mummer
docker pulls
  • 4.0.0
  • 4.0.0 + RGDv2
  • 4.0.0 + RGDv2 + gnuplot
https://github.com/mummer4/mummer
Mykrobe + Genotyphi + sonneityping
docker pulls
https://github.com/Mykrobe-tools/mykrobe
https://github.com/typhoidgenomics/genotyphi
https://github.com/katholt/sonneityping
NanoPlot
docker pulls
https://github.com/wdecoster/NanoPlot
ngmaster
docker pulls
  • 0.5.8
  • 1.0.0
https://github.com/MDU-PHL/ngmaster
NCBI Datasets
docker pulls
Click to see all datasets versions datasets versions
https://github.com/ncbi/datasets
https://www.ncbi.nlm.nih.gov/datasets/docs/v1/
NCBI AMRFinderPlus
docker pulls
AMRFinderPlus & database verion
Click to see AMRFinderplus v3.11.4 and older versions!
https://github.com/ncbi/amr
NCBI table2asn
docker pulls
https://www.ncbi.nlm.nih.gov/genbank/table2asn/
https://ftp.ncbi.nlm.nih.gov/asn1-converters/versions/2022-06-14/by_program/table2asn/
ONTime
docker pulls
https://github.com/mbhall88/ontime
OrthoFinder
docker pulls
  • 2.17
https://github.com/davidemms/OrthoFinder
Panaroo
docker pulls
(https://hub.docker.com/r/staphb/panaroo)
pango_aliasor
docker pulls
https://github.com/corneliusroemer/pango_aliasor
Pangolin
docker pulls
Click to see Pangolin v4.2 and older 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
Pangolin version & pangolin-data version
https://github.com/cov-lineages/pangolin
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
docker pulls
https://github.com/maxgmarin/panqc/releases/tag/0.4.0
parallel-perl
docker pulls
  • 20200722
https://www.gnu.org/software/parallel
parsnp
docker pulls
https://github.com/marbl/parsnp
pasty
docker pulls
https://github.com/rpetit3/pasty
pbmm2
docker pulls
https://github.com/PacificBiosciences/pbmm2
Pavian
docker pulls
https://github.com/fbreitwieser/pavian
pbptyper
docker pulls
https://github.com/rpetit3/pbptyper
pbtk
docker pulls
https://github.com/PacificBiosciences/pbtk
Phyml
docker pulls
  • 3.3.20220408
https://github.com/stephaneguindon/phyml
phyTreeViz
docker pulls
https://github.com/moshi4/phyTreeViz/
Piggy
docker pulls
  • 1.5
https://github.com/harry-thorpe/piggy
Pilon
docker pulls
  • 1.23.0
  • 1.24
https://github.com/broadinstitute/pilon
Piranha
docker pulls
  • 1.0.4
https://github.com/polio-nanopore/piranha
PlasmidFinder
docker pulls
https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/
PlasmidSeeker
docker pulls
  • 1.0
  • 1.3
https://github.com/bioinfo-ut/PlasmidSeeker
pmga
docker pulls
  • 3.0.2
https://github.com/rpetit3/pmga
PolkaPox
docker pulls
https://github.com/CDCgov/polkapox
polypolish
docker pulls
https://github.com/rrwick/Polypolish
PopPUNK
docker pulls
https://github.com/bacpop/PopPUNK
Porechop
docker pulls
  • 0.2.4
https://github.com/rrwick/Porechop
PPanGGOLiN
docker pulls
https://github.com/labgem/PPanGGOLiN
Prokka
docker pulls
  • 1.13.4
  • 1.14.0
  • 1.14.5
  • 1.14.6
https://github.com/tseemann/prokka
pyCirclize
docker pulls
https://github.com/moshi4/pyCirclize
pyGenomeViz
docker pulls
https://github.com/moshi4/pyGenomeViz
pyMLST
docker pulls
https://github.com/bvalot/pyMLST
pypolca
docker pulls
https://github.com/gbouras13/pypolca
QUAST
docker pulls
https://github.com/ablab/quast
QuickSNP
docker pulls
  • 1.0.1
https://github.com/k-florek/QuickSNP
racon
docker pulls
  • https://github.com/lbcb-sci/racon
  • https://github.com/isovic/racon (ARCHIVED)
  • rasusa
    docker pulls
    https://github.com/mbhall88/rasusa
    raven
    docker pulls
    https://github.com/lbcb-sci/raven
    RAxML
    docker pulls
    https://github.com/stamatak/standard-RAxML
    RAxML-NG
    docker pulls
    https://github.com/amkozlov/raxml-ng
    rdp
    docker pulls
    https://sourceforge.net/projects/rdp-classifier/files/rdp-classifier/rdp_classifier_2.14.zip/download
    ResFinder
    docker pulls
    https://bitbucket.org/genomicepidemiology/resfinder/src/master/
    Roary
    docker pulls
    • 3.12.0
    • 3.13.0
    https://github.com/sanger-pathogens/Roary
    SalmID
    docker pulls
    • 0.1.23
    https://github.com/hcdenbakker/SalmID
    samclip
    docker pulls
    https://github.com/tseemann/samclip
    Samtools
    docker pulls
    https://github.com/samtools/samtools
    SeqFu
    docker pulls
    https://github.com/telatin/seqfu2
    SeqKit
    docker pulls
    https://github.com/shenwei356/seqkit
    SeqSero
    docker pulls
    • 1.0.1
    https://github.com/denglab/SeqSero
    SeqSero2
    docker pulls
    https://github.com/denglab/SeqSero2/
    seqtk
    docker pulls
    https://github.com/lh3/seqtk
    seqyclean
    docker pulls
    • 1.10.09
    https://github.com/ibest/seqyclean
    Seroba
    docker pulls
    • 1.0.0
    • 1.0.2
    https://github.com/sanger-pathogens/seroba
    SerotypeFinder
    docker pulls
    https://bitbucket.org/genomicepidemiology/serotypefinder/
    ShigaPass
    docker pulls
    https://github.com/imanyass/ShigaPass
    shigatyper
    docker pulls
    https://github.com/CFSAN-Biostatistics/shigatyper
    ShigEiFinder
    docker pulls
    https://github.com/LanLab/ShigEiFinder
    Shovill
    docker pulls
    • 1.0.4
    • 1.1.0
    https://github.com/tseemann/shovill
    Shovill-se
    docker pulls
    • 1.1.0
    https://github.com/rpetit3/shovill/tree/v1.1.0se
    SISTR
    docker pulls
    • 1.0.2
    • 1.1.1
    https://github.com/phac-nml/sistr_cmd
    SKA
    docker pulls
    • 1.0
    https://github.com/simonrharris/SKA
    SKA2
    docker pulls
    https://github.com/bacpop/ska.rust
    skani
    docker pulls
    https://github.com/bluenote-1577/skani
    SKESA
    docker pulls
    https://github.com/ncbi/SKESA
    Smalt
    docker pulls
    • 0.7.6
    https://www.sanger.ac.uk/tool/smalt-0/
    snpeff
    docker pulls
    https://pcingola.github.io/SnpEff
    Snippy
    docker pulls
    • 4.4.5
    • 4.5.1
    • 4.6.0
    https://github.com/tseemann/snippy
    snp-dists
    docker pulls
    • 0.6.2
    • 0.8.2
    https://github.com/tseemann/snp-dists
    SNP-sites
    docker pulls
    • 2.3.3
    • 2.5.1
    https://github.com/sanger-pathogens/snp-sites
    SNVPhyl-tools
    docker pulls
    • 1.8.2
    https://github.com/phac-nml/snvphyl-tools
    SPAdes
    docker pulls
    https://github.com/ablab/spades
    http://cab.spbu.ru/software/spades/
    SRA-toolkit
    docker pulls
    https://github.com/ncbi/sra-tools
    SRST2
    docker pulls
    https://github.com/katholt/srst2
    Staramr
    docker pulls
    https://github.com/phac-nml/staramr
    stxtyper
    docker pulls
    https://github.com/ncbi/stxtyper
    sylph
    docker pulls
    https://github.com/bluenote-1577/sylph
    TBProfiler
    docker pulls
    https://github.com/jodyphelan/TBProfiler
    TipToft
    docker pulls
    • 1.0.0
    • 1.0.2
    https://github.com/andrewjpage/tiptoft
    Tostadas
    docker pulls
    https://github.com/CDCgov/tostadas
    Treemmer
    docker pulls
    • 0.3
    https://git.scicore.unibas.ch/TBRU/Treemmer (archived, moved to GitHub)
    https://github.com/fmenardo/Treemmer
    Trimmomatic
    docker pulls
    • 0.38
    • 0.39
    http://www.usadellab.org/cms/?page=trimmomatic
    https://github.com/usadellab/Trimmomatic
    Trycycler
    docker pulls
    https://github.com/rrwick/Trycycler
    Unicycler
    docker pulls
    • 0.4.7
    • 0.4.8
    • 0.4.9
    • 0.5.0
    https://github.com/rrwick/Unicycler
    VADR
    docker pulls
    https://github.com/nawrockie/vadr (archived, now redirects to ncbi/vadr)
    https://github.com/ncbi/vadr
    Verkko
    docker pulls
    https://github.com/marbl/verkko
    VIBRANT
    docker pulls
    • 1.2.1
    https://github.com/AnantharamanLab/VIBRANT
    VIGOR4
    docker pulls
    https://github.com/JCVenterInstitute/VIGOR4
    Viridian
    docker pulls
    https://github.com/iqbal-lab-org/viridian
    VirSorter2
    docker pulls
    • 2.1
    https://github.com/jiarong/VirSorter2
    VirulenceFinder
    docker pulls
    https://bitbucket.org/genomicepidemiology/virulencefinder/src/master/
    https://bitbucket.org/genomicepidemiology/virulencefinder_db/src/master/
    wtdbg2
    docker pulls
    • 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

    Authors/Maintainers

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