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Section: Software

GkArrays – indexing high throughput sequencer reads

Actively maintained.

Software self-assessment: A-3, SO-3, SM-3, EM-2, SDL-4, DA-4, CD-4, MS-4, TPM-3

Software web site : http://crac.gforge.inria.fr/gkarrays/

Objective : Gk-Arrays is a C++ library specifically dedicated to indexing reads produced by high-throughput sequencers. This index allows to answer queries centred on reads. It also takes benefits from the input specificity to lower space consumption.

This library is the result of a collaboration with N. Philippe and T. Commes (IGH laboratory, Montpellier), M. Léonard and T. Lecroq (LITIS laboratory, Rouen) and É. Rivals (LIRMM laboratory, Montpellier). We plan to improve our library in the forthcoming months with the help of Master's students.