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Algorithms Mol Biol. 2013 Sep 16;8(1):22. doi: 10.1186/1748-7188-8-22.

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

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Computer Science department, ENS Cachan / IRISA / INRIA, Rennes 35042, France.



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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