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

View ORCID ProfilePierre Marijon, Rayan Chikhi, Jean-Stéphane Varré
doi: https://doi.org/10.1101/674036
Pierre Marijon
1Inria, Univ. Lille, CNRS, Centrale Lille, UMR 9189 - CRIStAL, F-59000 Lille, France
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  • ORCID record for Pierre Marijon
  • For correspondence: pierre.marijon@inria.fr
Rayan Chikhi
2Institut Pasteur, C3BI USR 3756 IP CNRS, Paris, France
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Jean-Stéphane Varré
3Univ. Lille, CNRS, Centrale Lille, Inria, UMR 9189 - CRIStAL, F-59000 Lille, France
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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 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.

Footnotes

  • Important revision, we add many datasets (more than 60) in result and two figures to present how our tools work.

  • https://github.com/natir/yacrd-and-fpa-upstream-tools-for-lr-genome-assembly

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted March 02, 2020.
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yacrd and fpa: upstream tools for long-read genome assembly
Pierre Marijon, Rayan Chikhi, Jean-Stéphane Varré
bioRxiv 674036; doi: https://doi.org/10.1101/674036
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yacrd and fpa: upstream tools for long-read genome assembly
Pierre Marijon, Rayan Chikhi, Jean-Stéphane Varré
bioRxiv 674036; doi: https://doi.org/10.1101/674036

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