Genome Analysis Toolkit

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

The Genome Analysis Toolkit (GATK) is a structured programming framework designed to enable rapid development of efficient and robust analysis tools for next-generation DNA sequencers. 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