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

Rayan Chikhi 1, 2, * Guillaume Rizk 3
* Corresponding author
1 GenScale - Scalable, Optimized and Parallel Algorithms for Genomics
IRISA-D7 - GESTION DES DONNÉES ET DE LA CONNAISSANCE, Inria Rennes – Bretagne Atlantique
Abstract : Background
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).
Results
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.
Conclusions
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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Submitted on : Wednesday, October 2, 2013 - 5:40:08 AM
Last modification on : Thursday, January 20, 2022 - 5:33:13 PM
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Rayan Chikhi, Guillaume Rizk. Space-efficient and exact de Bruijn graph representation based on a Bloom filter. Algorithms for Molecular Biology, BioMed Central, 2013, 8 (1), pp.22. ⟨10.1186/1748-7188-8-22⟩. ⟨hal-00868805⟩

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