joelmartin Goto Github PK

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

mountblockd

Launch daemon blocking auto mounting of certain volumes

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.

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

samtools

test

setting up first repo