staphb/salmid

Sponsored OSS

By State Public Health Bioinformatics Community

Updated almost 6 years ago

Rapid confirmation of Salmonella spp. and subspp. from sequence data

Image
Data Science
Machine Learning & AI

636

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.

Each Dockerfile lists author/maintainer for that specific Docker image, but the authors/maintainers of the docker images are:

If you would like to contribute with your own Docker image or perhaps 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 User Guide

We have also created a user guide that outlines methods and best practices for using and developing docker containers.
Docker User Guide

Available Docker images

SoftwareVersionLink
seqyclean
docker pulls
1.10.09https://github.com/ibest/seqyclean
SalmID
docker pulls
0.1.23https://github.com/hcdenbakker/SalmID
mlst
docker pulls
2.16.2https://github.com/tseemann/mlst
SKESA
docker pulls
2.3.0https://github.com/ncbi/SKESA
FastANI
docker pulls
1.1https://github.com/ParBLiSS/FastANI
SRA-toolkit
docker pulls
2.9.2https://github.com/ncbi/sra-tools
Lyve-SET (includes CG-Pipeline scripts and raxml)
docker pulls
1.1.4f, 2.0.1 (lyve-SET)https://github.com/lskatz/lyve-SEThttps://github.com/lskatz/CG-Pipeline
Kraken
docker pulls
1.0https://github.com/DerrickWood/kraken
SPAdes
docker pulls
3.12.0, 3.13.0http://cab.spbu.ru/software/spades/
QUAST
docker pulls
5.0.0https://github.com/ablab/quast
Mash
docker pulls
2.1https://github.com/marbl/Mash
SerotypeFinder
docker pulls
1.1 (I think? Bitbucket repo does not list older versions like the one in this docker image)https://bitbucket.org/genomicepidemiology/serotypefinder/
SeqSero
docker pulls
1.0.1https://github.com/denglab/SeqSero
SeqSero2
docker pulls
0.1.0https://github.com/denglab/SeqSero2/
SISTR
docker pulls
1.0.2https://github.com/peterk87/sistr_cmd
ABRicate
docker pulls
0.8.7https://github.com/tseemann/abricate
Prokka
docker pulls
1.13https://github.com/tseemann/prokka
Trimmomatic
docker pulls
0.38http://www.usadellab.org/cms/?page=trimmomatic
iqtree
docker pulls
1.6.7http://www.iqtree.org/
Unicycler
docker pulls
0.4.7https://github.com/rrwick/Unicycler
Canu-Racon
docker pulls
1.7.1 (Canu) 1.3.1 (Racon) 2.13 (minimap2)https://canu.readthedocs.io/en/latest/https://github.com/isovic/raconhttps://lh3.github.io/minimap2/
Roary
docker pulls
3.12.0https://github.com/sanger-pathogens/Roary
CDC-SPN
docker pulls
0.1 (no version)https://github.com/BenJamesMetcalf/Spn_Scripts_Reference
Shovill
docker pulls
1.0.4https://github.com/tseemann/shovill
BWA
docker pulls
0.7.17https://github.com/lh3/bwa
Samtools
docker pulls
1.9https://github.com/samtools/samtools
cfsan-snp-pipeline
docker pulls
2.0.2https://github.com/CFSAN-Biostatistics/snp-pipeline

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

Docker Pull Command

docker pull staphb/salmid