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Journal Articles Genome Biology Year : 2021

Simplitigs as an efficient and scalable representation of de Bruijn graphs

Abstract

de Bruijn graphs play an essential role in bioinformatics, yet they lack a universal scalable representation. Here, we introduce simplitigs as a compact, efficient, and scalable representation, and ProphAsm, a fast algorithm for their computation. For the example of assemblies of model organisms and two bacterial pan-genomes, we compare simplitigs to unitigs, the best existing representation, and demonstrate that simplitigs provide a substantial improvement in the cumulative sequence length and their number. When combined with the commonly used Burrows-Wheeler Transform index, simplitigs reduce memory, and index loading and query times, as demonstrated with large-scale examples of GenBank bacterial pan-genomes.
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Dates and versions

hal-03049400 , version 1 (09-12-2020)

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Karel Brinda, Michael Baym, Gregory Kucherov. Simplitigs as an efficient and scalable representation of de Bruijn graphs. Genome Biology, 2021, 22 (96), ⟨10.1101/2020.01.12.903443⟩. ⟨hal-03049400⟩
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