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bioRxiv · 10.1101/2021.12.14.472718

Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2

Khan, J.·Kokot, M.·Deorowicz, S.·Patro, R.
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Abstract

The de Bruijn graph is a key data structure in modern computational genomics, and construction of its compacted variant resides upstream of many genomic analyses. As the quantity of genomic data grows rapidly, this often forms a computational bottleneck. We present CO_SCPLOWUTTLEFISHC_SCPLOW 2, significantly advancing the state-of-the-art for this problem. On a commodity server, it reduces the graph construction time for 661K bacterial genomes, of size 2.58Tbp, from 4.5 days to 17-23 hours; and it constructs the graph for 1.52Tbp white spruce reads in [~]10 hours, while the closest competitor requires 54-58 hours, using considerably more memory.

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Khan, J., Kokot, M., Deorowicz, S., Patro, R.. 2021-12-16. Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2. https://doi.org/10.1101/2021.12.14.472718

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