Space-efficient and exact de Bruijn graph representation based on a Bloom filter

Rayan Chikhi 1, 2, * Guillaume Rizk 3
* Corresponding author
2 GenScale - Scalable, Optimized and Parallel Algorithms for Genomics
Inria Rennes – Bretagne Atlantique , IRISA-D7 - GESTION DES DONNÉES ET DE LA CONNAISSANCE
Abstract : The de Bruijn graph data structure is widely used in next-generation sequencing (NGS). Many programs, e.g. de novo assemblers, rely on in-memory representation of this graph. However, current techniques for representing the de Bruijn graph of a human genome require a large amount of memory (> 30 GB). We propose a new encoding of the de Bruijn graph, which occupies an order of magnitude less space than current representations. The encoding is based on a Bloom filter, with an additional structure to remove critical false positives. An assembly software implementing this structure, Minia, performed a complete de novo assembly of human genome short reads using 5.7 Gb of memory in 23 hours.
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Conference papers
WABI 2012, Sep 2012, Ljubljana, Slovenia. 7534, pp 236-248, 2012, <10.1007/978-3-642-33122-0_19>


https://hal.archives-ouvertes.fr/hal-00753930
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Submitted on : Monday, November 19, 2012 - 10:53:47 PM
Last modification on : Tuesday, May 19, 2015 - 1:02:30 AM

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Rayan Chikhi, Guillaume Rizk. Space-efficient and exact de Bruijn graph representation based on a Bloom filter. WABI 2012, Sep 2012, Ljubljana, Slovenia. 7534, pp 236-248, 2012, <10.1007/978-3-642-33122-0_19>. <hal-00753930>

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