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Read indexing

Nicolas Philippe 1 Mikael Salson 2 Thierry Lecroq 3 Martine Léonard 3 Thérèse Commes 4 Eric Rivals 1, *
* Corresponding author
1 MAB - Méthodes et Algorithmes pour la Bioinformatique
LIRMM - Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier
2 BONSAI - Bioinformatics and Sequence Analysis
LIFL - Laboratoire d'Informatique Fondamentale de Lille, Inria Lille - Nord Europe
Abstract : The question of read indexing remains broadly unexplored. However, the increase in sequence throughput urges for new algorithmic solutions to query large read collections efficiently. We pro- pose a solution, named Gk arrays, to index large collections of reads, an algorithm to build the structure, and procedures to query it. Once constructed, the index structure is kept in main memory and is repeatedly accessed to answer various types of queries. We compare our data structure to other possible solutions to investigate its scalability and computational efficiency. Gk arrays are im- plemented in a general purpose library, which may prove useful for assembly purposes, for evaluating the expression level in RNA-seq, and others high throughput sequencing applications.
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https://hal-lirmm.ccsd.cnrs.fr/lirmm-00757983
Contributor : Eric Rivals <>
Submitted on : Tuesday, November 27, 2012 - 6:14:57 PM
Last modification on : Friday, September 17, 2021 - 3:27:13 AM
Long-term archiving on: : Saturday, December 17, 2016 - 4:12:35 PM

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Nicolas Philippe, Mikael Salson, Thierry Lecroq, Martine Léonard, Thérèse Commes, et al.. Read indexing. EMBnet.journal, EMBnet, 2011, 17 (Supplement B), pp.1. ⟨10.14806/ej.17.B.289⟩. ⟨lirmm-00757983⟩

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