markdunning/ngs-sandbox repository overview

This is an attempt to create a collection of popular Next-Generation Sequencing processing tools for teaching / training purposes. Novice users can try out the tools without having to install or fear of breaking their own machine or a server.

Software was downloaded to /software/. The current list includes

• samtools

samtools 1.1 compiled from source installed into /usr/bin/

• bwa

bwa 0.7.12 compiled from source installed into /usr/bin/

• fastqc

fastqc 0.11.2 compiled binary

• picard

picard-tools 1.119 compiled binary

• bedtools

installed using apt-get install

• vcftools (http://vcftools.sourceforge.net/⁠)

vctools 0.1.12b compiled from source

• bowtie2

compiled from git

• tophat

tophat 1.3.2 compiled binary

• trimmomatic (http://www.usadellab.org/cms/?page=trimmomatic⁠)

trimmomatic 0.32 compiled binary

• samstat (http://samstat.sourceforge.net/⁠)

samstat 1.5 compiled from source

• fastx-toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html⁠)

installed via apt-get install

• sra-toolkit

version 2.4.3 binary