Software	Installation instructions	Codebase
eHive	http://www.ensembl.org/info/docs/api/api_git.html	https://github.com/Ensembl/ensembl-compara
ReseqTrack	https://github.com/EMBL-EBI-GCA/reseqtrack/blob/master/docs/ alignment_pipeline.txt	https://github.com/EMBL-EBI-GCA/reseqtrack
BWA-MEM	https://github.com/lh3/bwa/blob/master/bwakit/README.md	https://github.com/lh3/bwa
BioBamBam	https://github.com/gt1/biobambam2/blob/master/README.md	https://github.com/gt1/biobambam2
GATK	https://www.broadinstitute.org/gatk/download/	https://github.com/broadgsa/gatk-protected/
CRAMTools	http://www.ebi.ac.uk/ena/software/cram-toolkit	https://github.com/enasequence/cramtools