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
Inria Rennes – Bretagne Atlantique , IRISA-D7 - GESTION DES DONNÉES ET DE LA CONNAISSANCE
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.
Document type :
Journal articles
Complete list of metadatas

Cited literature [23 references]  Display  Hide  Download

https://hal.inria.fr/hal-00868805
Contributor : Ed. Bmc <>
Submitted on : Wednesday, October 2, 2013 - 5:40:08 AM
Last modification on : Thursday, November 15, 2018 - 11:57:53 AM
Long-term archiving on : Friday, January 3, 2014 - 4:32:03 AM

Files

1748-7188-8-22.pdf
Publisher files allowed on an open archive

Identifiers

Citation

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⟩

Share

Metrics

Record views

923

Files downloads

1046