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bioRxiv · 10.1101/2020.12.10.420448

Assembling Long Accurate Reads Using de Bruijn Graphs

Bankevich, A.·Bzikadze, A. V.·Kolmogorov, M.·Pevzner, P.
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Abstract

Although most existing genome assemblers are based on the de Bruijn graphs, it remains unclear how to construct these graphs for large genomes and large k-mer sizes. This algorithmic challenge has become particularly important with the emergence of long high-fidelity (HiFi) reads that were recently utilized to generate a semi-manual telomere-to-telomere assembly of the human genome and to get a glimpse into biomedically important regions that evaded all previous attempts to sequence them. To enable automated assemblies of long and accurate reads, we developed a fast LJA algorithm that reduces the error rate in these reads by three orders of magnitude (making them nearly error-free) and constructs the de Bruijn graph for large genomes and large k-mer sizes. Since the de Bruijn graph constructed for a fixed k-mer size is typically either too tangled or too fragmented, LJA uses a new concept of a multiplex de Bruijn graph with varying k-mer sizes. We demonstrate that LJA improves on the state-of-the-art assemblers with respect to both accuracy and contiguity and enables automated telomere-to-telomere assemblies of entire human chromosomes.

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Bankevich, A., Bzikadze, A. V., Kolmogorov, M., Pevzner, P.. 2020-12-11. Assembling Long Accurate Reads Using de Bruijn Graphs. https://doi.org/10.1101/2020.12.10.420448

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