Gatk

Record added by Jurg Ott (the original Rockefeller list)

Genome Analysis ToolKit

The GATK is a structured software library that makes writing efficient analysis tools using next-generation sequencing data very easy, and second it’s a suite of tools for working with human medical resequencing projects such as 1000 Genomes and The Cancer Genome Atlas. These tools include things like a depth of coverage analyzers, a quality score recalibrator, a SNP/indel caller and a local realigner.

Mark DePristo et al. (Broad Institute)

http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit

DePristo, Banks, Poplin, Garimella, Maguire, Hartl, Philippakis, del Angel, Rivas, Hanna, McKenna, Fennell, Kernytsky, Sivachenko, Cibulskis, Gabriel, Altshuler, Daly (2011), “A framework for variation discovery and genotyping using next-generation DNA sequencing data”, Nature Genetics, 43:491-498.