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NextPolish: a fast and efficient genome polishing tool for long-read assembly

Bioinformatics, 2020-04, Vol.36 (7), p.2253-2255 [Peer Reviewed Journal]

The Author(s) 2019. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com 2019 ;The Author(s) 2019. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com. ;ISSN: 1367-4803 ;EISSN: 1460-2059 ;EISSN: 1367-4811 ;DOI: 10.1093/bioinformatics/btz891 ;PMID: 31778144

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  • Title:
    NextPolish: a fast and efficient genome polishing tool for long-read assembly
  • Author: Hu, Jiang ; Fan, Junpeng ; Sun, Zongyi ; Liu, Shanlin
  • Berger, Bonnie
  • Is Part Of: Bioinformatics, 2020-04, Vol.36 (7), p.2253-2255
  • Description: Abstract Motivation Although long-read sequencing technologies can produce genomes with long contiguity, they suffer from high error rates. Thus, we developed NextPolish, a tool that efficiently corrects sequence errors in genomes assembled with long reads. This new tool consists of two interlinked modules that are designed to score and count K-mers from high quality short reads, and to polish genome assemblies containing large numbers of base errors. Results When evaluated for the speed and efficiency using human and a plant (Arabidopsis thaliana) genomes, NextPolish outperformed Pilon by correcting sequence errors faster, and with a higher correction accuracy. Availability and implementation NextPolish is implemented in C and Python. The source code is available from https://github.com/Nextomics/NextPolish. Supplementary information Supplementary data are available at Bioinformatics online.
  • Publisher: England: Oxford University Press
  • Language: English
  • Identifier: ISSN: 1367-4803
    EISSN: 1460-2059
    EISSN: 1367-4811
    DOI: 10.1093/bioinformatics/btz891
    PMID: 31778144
  • Source: Journals@Ovid Open Access Journal Collection Rolling
    Geneva Foundation Free Medical Journals at publisher websites
    PubMed Central
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