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GATB: Genome Assembly & Analysis Tool Box.

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.

SUBMITTER: Drezen E

PROVIDER: S-EPMC4184257 | biostudies-literature | 2014 Oct

REPOSITORIES: biostudies-literature

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GATB: Genome Assembly & Analysis Tool Box.

Drezen Erwan E Rizk Guillaume G Chikhi Rayan R Deltel Charles C Lemaitre Claire C Peterlongo Pierre P Lavenier Dominique D

Bioinformatics (Oxford, England) 20140701 20

<h4>Motivation</h4>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.<h4>Results</h4>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-Brui ...[more]

PMID: 24990603

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