GATB: Genome Assembly & Analysis Tool Box

Motivation: Efficient and fast next-generation sequencing (NGS) algorithms are essential to analyze the terabytes of data generated by the NGS machines. A serious bottleneck can be the design of such algorithms, as they require sophisticated data structures and advanced hardware implementation. Results: We propose an open-source library dedicated to genome assembly and analysis to fasten the process of developing efficient software. The library is based on a recent optimized de-Bruijn graph implementation allowing complex genomes to be processed on desktop computers using fast algorithms with low memory footprints. Availability and implementation: The GATB library is written in C++ and is available at the following Web site http://gatb.inria.fr under the A-GPL license. Contact: lavenier@irisa.fr Supplementary information: Supplementary data are available at Bioinformatics online.