GATB

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.

GATB: Genome Assembly & Analysis Tool Box.

GATB is an open-source library that focuses on genome assembly and analysis to speed up the development of efficient next-generation sequencing (NGS) algorithms. It is based on an optimized de-Bruijn graph implementation that allows complex genomes to be processed on desktop computers using fast algorithms with low memory footprints.

GATB

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