GATK 

The GATK is a structured software library that makes writing efficient analysis tools using next-generation sequencing data very easy. These tools include things like a depth of coverage analyzers, a quality score recalibrator, a SNP/indel caller and a local realigner. Robust, production-quality development library that underlies tools for common analysis problems (like SNP calling) as well as enabling exploratory research on NGS data. The GATK solves the data management challenge by separating data access patterns from analysis algorithms, using the functional programming philosophy of Map/Reduce. Consequently, the GATK is structured into data traversals and data walkers that interact through a programming contract in which the traversal provides a series of units of data to the walker, and the walker consumes each datum to generate an output for each datum. (http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Too... )