Introduction

Methods to reliably assess the accuracy of genome sequence data are lacking. Currently completeness is only described qualitatively and mis-assemblies are overlooked. Here we present REAPR, a tool that precisely identifies errors in genome assemblies without the need for a reference sequence. We have validated REAPR on complete genomes or de novo assemblies from bacteria, malaria and Caenorhabditis elegans, and demonstrate that 86% and 82% of the human and mouse reference genomes are error-free, respectively. When applied to an ongoing genome project, REAPR provides corrected assembly statistics allowing the quantitative comparison of multiple assemblies. REAPR is available at http://www.sanger.ac.uk/resources/software/reapr/.

Publications

  1. REAPR: a universal tool for genome assembly evaluation.
    Cite this
    Hunt M, Kikuchi T, Sanders M, Newbold C, Berriman M, Otto TD, 2013-05-01 - Genome biology

Credits

  1. Martin Hunt
    Developer

  2. Taisei Kikuchi
    Developer

  3. Mandy Sanders
    Developer

  4. Chris Newbold
    Developer

  5. Matthew Berriman
    Developer

  6. Thomas D Otto
    Investigator

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Summary
AccessionBT000381
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByThomas D Otto