Pierre Marijon1, Rayan Chikhi2, Jean-Stéphane Varré3. 1. Department of Computer Science, Inria, Univ. Lille, CNRS, Centrale Lille, UMR 9189 - CRIStAL, Lille F-59000, France. 2. Department of Computational Biology, Institut Pasteur, C3BI USR 3756 IP CNRS, Paris, France. 3. Univ. Lille, CNRS, Centrale Lille, UMR 9189 - CRIStAL - Centre de Recherche en Informatique Signal et Automatique de Lille, F-59000 Lille, France.
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.
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.
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