PT  - JOURNAL ARTICLE
AU  - Pierre Marijon
AU  - Rayan Chikhi
AU  - Jean-Stéphane Varré
TI  - yacrd and fpa: upstream tools for long-read genome assembly
AID  - 10.1101/674036
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 674036
4099  - http://biorxiv.org/content/early/2019/06/18/674036.short
4100  - http://biorxiv.org/content/early/2019/06/18/674036.full
AB  - 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, to respectively perform chimera removal/read scrubbing, and filter out spurious overlaps. We show that yacrd results in higher-quality assemblies and is two orders of magnitude faster than the best available alternative.Availability https://github.com/natir/yacrd and https://github.com/natir/fpaContact pierre.marijon{at}inria.frSupplementary information Supplementary data are available online.