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Erschienen in:
2012 | OriginalPaper | Buchkapitel
Space-Efficient and Exact de Bruijn Graph Representation Based on a Bloom Filter
verfasst von : Rayan Chikhi, Guillaume Rizk
Erschienen in: Algorithms in Bioinformatics
Verlag: Springer Berlin Heidelberg
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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.