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Conference Papers Lecture Notes in Computer Science Year : 2012

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

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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Dates and versions

hal-00753930 , version 1 (19-11-2012)

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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. pp 236-248, ⟨10.1007/978-3-642-33122-0_19⟩. ⟨hal-00753930⟩
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