staphb/trimmomatic

staphb/trimmomatic repository overview

⁠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

(Build only reflects those containers that have been added to the TravisCI tests)

Software	Version	Link
ABRicate⁠	0.8.7, 0.8.13, 0.8.13s (+serotypefinder db)	https://github.com/tseemann/abricate⁠
BWA⁠	0.7.17	https://github.com/lh3/bwa⁠
Canu-Racon⁠	1.7.1 (Canu) 1.3.1 (Racon) 2.13 (minimap2)	https://canu.readthedocs.io/en/latest/⁠ https://github.com/isovic/racon⁠ https://lh3.github.io/minimap2/⁠
CDC-SPN⁠	0.1 (no version)	https://github.com/BenJamesMetcalf/Spn_Scripts_Reference⁠
cfsan-snp-pipeline⁠	2.0.2	https://github.com/CFSAN-Biostatistics/snp-pipeline⁠
FastANI⁠	1.1	https://github.com/ParBLiSS/FastANI⁠
Flye⁠	2.5	https://github.com/fenderglass/Flye⁠
iqtree⁠	1.6.7	http://www.iqtree.org/⁠
Kraken⁠	1.0, 1.1.1	https://github.com/DerrickWood/kraken⁠
kSNP3⁠	3.1	https://sourceforge.net/projects/ksnp/⁠
Lyve-SET (includes CG-Pipeline scripts and raxml)⁠	1.1.4f, 2.0.1 (lyve-SET)	https://github.com/lskatz/lyve-SET⁠ https://github.com/lskatz/CG-Pipeline⁠
Mash⁠	2.1	https://github.com/marbl/Mash⁠
mashtree⁠	0.52.0	https://github.com/lskatz/mashtree⁠
medaka⁠	0.8.1	https://github.com/nanoporetech/medaka⁠
mlst⁠	2.16.2	https://github.com/tseemann/mlst⁠
Prokka⁠	1.13.4, 1.14.0	https://github.com/tseemann/prokka⁠
QUAST⁠	5.0.0, 5.0.2	https://github.com/ablab/quast⁠
Roary⁠	3.12.0	https://github.com/sanger-pathogens/Roary⁠
SalmID⁠	0.1.23	https://github.com/hcdenbakker/SalmID⁠
Samtools⁠	1.9	https://github.com/samtools/samtools⁠
SeqSero⁠	1.0.1	https://github.com/denglab/SeqSero⁠
SeqSero2⁠	0.1.0, 1.0.0	https://github.com/denglab/SeqSero2/⁠
seqyclean⁠	1.10.09	https://github.com/ibest/seqyclean⁠
SerotypeFinder⁠	1.1 (I think? Bitbucket repo does not list older versions like the one in this docker image)	https://bitbucket.org/genomicepidemiology/serotypefinder/⁠
Shovill⁠	1.0.4	https://github.com/tseemann/shovill⁠
SISTR⁠	1.0.2	https://github.com/peterk87/sistr_cmd⁠
SKESA⁠	2.3.0	https://github.com/ncbi/SKESA⁠
snp-dists⁠	0.6.2	https://github.com/tseemann/snp-dists⁠
SPAdes⁠	3.12.0, 3.13.0	http://cab.spbu.ru/software/spades/⁠
SRA-toolkit⁠	2.9.2	https://github.com/ncbi/sra-tools⁠
Staramr⁠	0.5.1	https://github.com/phac-nml/staramr⁠
Trimmomatic⁠	0.38, 0.39	http://www.usadellab.org/cms/?page=trimmomatic⁠
Unicycler⁠	0.4.7	https://github.com/rrwick/Unicycler⁠