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

Abstract

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. 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. https://github.com/natir/yacrd and https://github.com/natir/fpa. Supplementary data are available at Bioinformatics online.