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yacrd and fpa: upstream tools for long-read genome assembly

By Pierre Marijon, Rayan Chikhi, Jean-Stéphane Varré

Posted 18 Jun 2019
bioRxiv DOI: 10.1101/674036

Motivation Genome assembly is increasingly performed on long, uncorrected reads. Assembly quality may be degraded due to unfiltered chimeric reads; also, the storage of all read overlaps can take up to terabytes of disk space. Results We introduce two tools, yacrd and fpa, preform respectively chimera removal, read scrubbing, and filter out spurious overlaps. We show that yacrd results in higher-quality assemblies and is one hundred times faster than the best available alternative. Availability <https://github.com/natir/yacrd> and <https://github.com/natir/fpa> Contact pierre.marijon{at}inria.fr Supplementary information Supplementary data are available online.

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