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. 2014 Oct 15;30(20):2959-61.
doi: 10.1093/bioinformatics/btu406. Epub 2014 Jul 1.

GATB: Genome Assembly & Analysis Tool Box

Erwan Drezen  1 , Guillaume Rizk  1 , Rayan Chikhi  1 , Charles Deltel  1 , Claire Lemaitre  1 , Pierre Peterlongo  1 , Dominique Lavenier  1
Affiliations

GATB: Genome Assembly & Analysis Tool Box

Erwan Drezen et al. Bioinformatics. .

Abstract

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.

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Figures

Fig. 1.
Fig. 1.
Schematic view of the GATB organization
See this image and copyright information in PMC

References

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