Joel Martin's repositories
bcftools
This is the official development repository for BCFtools. To compile, the develop branch of htslib is needed: git clone --branch=develop git://github.com/samtools/htslib.git htslib
CNVnator
a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
gatk-protected
GATK Official Release Repository: contains the core MIT-licensed GATK framework, plus "protected" tools restricted to non-commercial use only
hwraid
HWRaid: Free code from http://hwraid.le-vert.net
jgi_kbase_integration_tests
Test code for testing jgi kbase integration, from data import through assembly.
memtime
Measure time and memory consumption. copied from http://www.update.uu.se/~johanb/memtime/
metasv
MetaSV: An accurate and integrative structural-variant caller for next generation sequencing
pindel
Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.
mountblockd
Launch daemon blocking auto mounting of certain volumes
pindel2vcfplay
pulling apart pindel2vcf to see how it works because its unhappy with our weird plant 30,000+ contig genomes
sambamba
Tools for working with SAM/BAM/CRAM data