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

Abstract

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 for chimera removal and read scrubbing, and fpa for filtering out spurious overlaps. We show that yacrd results in higher-quality assemblies and is one hundred times faster than the best available alternative.

Availability and implementation: https://github.com/natir/yacrd and https://github.com/natir/fpa.

Supplementary information: Supplementary data are available at Bioinformatics online.