GATB: Genome Assembly & Analysis Tool Box

Abstract : Motivation: Efficient and fast NGS algorithms are essential to ana-lyze the terabytes of data generated by the next generation se-quencing machines. A serious bottleneck can be the design of such algorithms, as they require sophisticated data structures and ad-vanced 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 very 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.
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https://hal.archives-ouvertes.fr/hal-01088571
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Submitted on : Monday, December 1, 2014 - 3:51:13 PM
Last modification on : Wednesday, July 10, 2019 - 7:14:02 PM
Long-term archiving on : Monday, March 2, 2015 - 1:26:56 PM

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Erwan Drezen, Guillaume Rizk, Rayan Chikhi, Charles Deltel, Claire Lemaitre, et al.. GATB: Genome Assembly & Analysis Tool Box. Bioinformatics, Oxford University Press (OUP), 2014, 30, pp.2959 - 2961. ⟨10.1093/bioinformatics/btu406⟩. ⟨hal-01088571⟩

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