nbutter/gatk_tools repository overview

⁠fastq2bam

GATK and other bioinformatics tools packaged together.

If you make use of this image, please acknowledge Sydney Informatics Hub at the University of Sydney https://informatics.sydney.edu.au/⁠

⁠Build with:

sudo docker build . -t gatk

or on singularity:

singularity pull docker://nbutter/gatk_tools

⁠Run with something like:

sudo docker run --rm -it -v `pwd`:/workspace gatk

Or on Windows

docker run --rm -it -v C:\WORK\ShortProjects\GATK:/workspace gatk

⁠Java

openjdk version "1.8.0_191"

OpenJDK Runtime Environment (build 1.8.0_191-8u191-b12-0ubuntu0.16.04.1-b12)

OpenJDK 64-Bit Server VM (build 25.191-b12, mixed mode)

https://openjdk.java.net/⁠

⁠GATK

The Genome Analysis Toolkit (GATK) v4.1.2.0

HTSJDK Version: 2.19.0

Picard Version: 2.19.0

https://software.broadinstitute.org/gatk/download/⁠

⁠Samtools

Version: 0.1.19-96b5f2294a

http://www.htslib.org/⁠

⁠fastp

fastp 0.20.0

https://github.com/OpenGene/fastp⁠

⁠BWA

Version: 0.7.15-r1140

http://bio-bwa.sourceforge.net/⁠

https://github.com/lh3/bwa⁠

⁠Sambamba

sambamba 0.7.0

LDC 1.10.0 / DMD v2.080.1 / LLVM6.0.1 / bootstrap LDC - the LLVM D compiler (0.17.4)

https://lomereiter.github.io/sambamba/⁠