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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

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
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
Augur
docker pulls
  • 6.3.0
  • 7.0.2
  • 8.0.0
  • 9.0.0
  • 16.0.3
https://github.com/nextstrain/augur
Auspice
docker pulls
  • 2.12.0
https://github.com/nextstrain/auspice
BBTools
docker pulls
  • 38.76
  • 38.86
  • 38.95
  • 38.96
  • 38.97
  • 38.98
  • 38.99
  • 39.00
  • 39.01
https://jgi.doe.gov/data-and-tools/bbtools/
bcftools
docker pulls
  • 1.10.2
  • 1.11
  • 1.12
  • 1.13
  • 1.14
  • 1.15
  • 1.16
  • 1.17
  • 1.18
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
  • 2.4.4
  • 2.4.5
  • 2.5.1
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
  • 5.4.7
https://busco.ezlab.org/busco_userguide.html
https://gitlab.com/ezlab/busco
BWA
docker pulls
  • 0.7.17
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
Circlator
docker pulls
  • 1.5.6
  • 1.5.5
https://github.com/sanger-pathogens/circlator
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
dnaapler
docker pulls
https://github.com/gbouras13/dnaapler
dragonflye
docker pulls
https://github.com/rpetit3/dragonflye
Dr. PRG
docker pulls
https://mbh.sh/drprg/
DSK
docker pulls
  • 0.0.100
https://gatb.inria.fr/software/dsk/
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
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/
GenoVi
docker pulls
https://github.com/robotoD/GenoVi
gfastats
docker pulls
  • 1.3.6
https://github.com/vgl-hub/gfastats
hmmer
docker pulls
http://hmmer.org/
homopolish
docker pulls
  • 0.4.1
https://github.com/ythuang0522/homopolish/
htslib
docker pulls
  • 1.14
  • 1.15
  • 1.16
  • 1.17
  • 1.18
https://www.htslib.org/
iqtree
docker pulls
  • 1.6.7
http://www.iqtree.org/
iqtree2
docker pulls
http://www.iqtree.org/
IRMA
docker pulls
  • 1.0.2
  • 1.0.3
  • 1.1.2
  • 1.1.3
https://wonder.cdc.gov/amd/flu/irma/
isPcr
docker pulls
https://users.soe.ucsc.edu/~kent/
iVar
docker pulls
  • 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
https://github.com/andersen-lab/ivar
Kaptive
docker pulls
  • 2.0.0
  • 2.0.3
  • 2.0.5
https://github.com/katholt/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)
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
kSNP3
docker pulls
  • 3.1
https://sourceforge.net/projects/ksnp/
kSNP4
docker pulls
  • 4.0
https://sourceforge.net/projects/ksnp/
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
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
  • 7.450
  • 7.475
  • 7.505
https://mafft.cbrc.jp/alignment/software/
Mash
docker pulls
  • 2.1
  • 2.2
  • 2.3
https://github.com/marbl/Mash
mashtree
docker pulls
  • 0.52.0
  • 0.57.0
  • 1.0.4
  • 1.2.0
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
  • 0.8.1
  • 1.0.1
  • 1.2.0
https://github.com/nanoporetech/medaka
metaphlan
docker pulls
  • 3.0.3-no-db (no database)
  • 3.0.3 (~3GB db)
https://github.com/biobakery/MetaPhlAn/tree/3.0
MIDAS
docker pulls
  • 1.3.2 (no database)
https://github.com/snayfach/MIDAS
minimap2
docker pulls
  • 2.17
  • 2.18
  • 2.21
  • 2.22
  • 2.23
  • 2.24
  • 2.25
  • 2.26
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
  • 1.7
  • 1.8
https://github.com/ewels/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
  • 1.27.0
  • 1.29.0
  • 1.30.1
  • 1.32.0
  • 1.33.0
  • 1.40.0
  • 1.41.6
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
  • 1.26.678
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)
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)
parallel-perl
docker pulls
  • 20200722
https://www.gnu.org/software/parallel
pasty
docker pulls
https://github.com/rpetit3/pasty
Pavian
docker pulls
https://github.com/fbreitwieser/pavian
pbptyper
docker pulls
  • 1.0.0
  • 1.0.1
  • 1.0.4
https://github.com/rpetit3/pbptyper
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
  • 2.1.6
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
polypolish
docker pulls
  • 0.5.0
https://github.com/rrwick/Polypolish
PopPUNK
docker pulls
https://github.com/bacpop/PopPUNK
Porechop
docker pulls
  • 0.2.4
https://github.com/rrwick/Porechop
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
QUAST
docker pulls
https://github.com/ablab/quast
QuickSNP
docker pulls
  • 1.0.1
https://github.com/k-florek/QuickSNP
racon
docker pulls
  • 1.4.3
  • 1.4.20
https://github.com/lbcb-sci/racon
https://github.com/isovic/racon (ARCHIVED)
rasusa
docker pulls
  • 0.1.0
  • 0.2.0
  • 0.3.0
  • 0.6.0
  • 0.7.0
https://github.com/mbhall88/rasusa
raven
docker pulls
https://github.com/lbcb-sci/raven
RAxML
docker pulls
  • 8.2.12 (RAxML) and 0.9.0 (RAxML Next Generation)
https://github.com/stamatak/standard-RAxML
https://github.com/amkozlov/raxml-ng
ResFinder
docker pulls
  • 4.1.1
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
Samtools
docker pulls
https://github.com/samtools/samtools
SeqKit
docker pulls
  • 2.3.1
https://github.com/shenwei356/seqkit
SeqSero
docker pulls
  • 1.0.1
https://github.com/denglab/SeqSero
SeqSero2
docker pulls
  • 0.1.0
  • 1.0.0
  • 1.0.2
  • 1.1.0
  • 1.1.1
  • 1.2.1
https://github.com/denglab/SeqSero2/
seqtk
docker pulls
  • 1.3
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
  • 1.1 (perl version)
  • 2.0.1 (python version)
https://bitbucket.org/genomicepidemiology/serotypefinder/
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
skani
docker pulls
https://github.com/bluenote-1577/skani
SKESA
docker pulls
  • 2.3.0
  • 2.4.0 (gfa_connector & kmercounter included)
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
  • 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
https://github.com/ablab/spades
http://cab.spbu.ru/software/spades/
SRA-toolkit
docker pulls
  • 2.9.2
https://github.com/ncbi/sra-tools
SRST2
docker pulls
https://github.com/katholt/srst2
Staramr
docker pulls
  • 0.5.1
  • 0.7.1
  • 0.8.0
https://github.com/phac-nml/staramr
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
  • 0.2.0-beta
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
  • 0.3.1
  • 0.3.2
  • 0.3.3
  • 0.5.0
  • 0.5.3
  • 0.5.4
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
  • 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
https://github.com/nawrockie/vadr (archived, now redirects to ncbi/vadr)
https://github.com/ncbi/vadr
VIBRANT
docker pulls
  • 1.2.1
https://github.com/AnantharamanLab/VIBRANT
VIGOR4
docker pulls
  • 4.1.20190131
https://github.com/JCVenterInstitute/VIGOR4
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:

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