ksimons77

Container with both fastx and sickle to enable demultiplexing, index trimming, and quality trimming

http://bio-bwa.sourceforge.net/ Mapping reads to a reference sequence

Combine samtools and bwa http://www.htslib.org/ http://bio-bwa.sourceforge.net/

http://varscan.sourceforge.net/ SNP calling

http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

https://github.com/najoshi/sickle sickle adaptive trimmer

https://github.com/samtools/samtools/

https://github.com/agordon/fastx_toolkit

GATK 3.6 from Broad Institute

picard