Unknown

Dataset Information

0

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

altmetric image

Publications

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]

Similar Datasets

| S-EPMC3798757 | biostudies-literature
| S-EPMC7074766 | biostudies-literature
| S-EPMC6203371 | biostudies-literature
| S-EPMC5083241 | biostudies-literature
| S-EPMC9825286 | biostudies-literature
| S-EPMC4237348 | biostudies-literature
| S-EPMC5408032 | biostudies-literature
| S-EPMC5466706 | biostudies-literature
| PRJEB50026 | ENA
| S-EPMC5249034 | biostudies-literature