A resource-frugal probabilistic dictionary and applications in (meta)genomics

Camille Marchet 1 Antoine Limasset 1 Lucie Bittner 2 Pierre Peterlongo 1
1 GenScale - Scalable, Optimized and Parallel Algorithms for Genomics
Inria Rennes – Bretagne Atlantique , IRISA-D7 - GESTION DES DONNÉES ET DE LA CONNAISSANCE
Abstract : Genomic and metagenomic fields, generating huge sets of short genomic sequences, brought their own share of high performance problems. To extract relevant pieces of information from the huge data sets generated by current sequencing techniques, one must rely on extremely scalable methods and solutions. Indexing billions of objects is a task considered too expensive while being a fundamental need in this field. In this paper we propose a straightforward indexing structure that scales to billions of element and we propose two direct applications in genomics and metagenomics. We show that our proposal solves problem instances for which no other known solution scales-up. We believe that many tools and applications could benefit from either the fundamental data structure we provide or from the applications developed from this structure.
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https://hal.inria.fr/hal-01322440
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Submitted on : Friday, May 27, 2016 - 11:00:32 AM
Last modification on : Tuesday, January 29, 2019 - 10:02:08 PM
Long-term archiving on : Sunday, August 28, 2016 - 10:35:23 AM

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  • HAL Id : hal-01322440, version 1
  • ARXIV : 1605.08319

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Camille Marchet, Antoine Limasset, Lucie Bittner, Pierre Peterlongo. A resource-frugal probabilistic dictionary and applications in (meta)genomics. 2016. ⟨hal-01322440⟩

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