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)
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.