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Murphy RR, O'Connell J, Cox AJ, et al. NxRepair: error correction in de novo sequence assembly using Nextera mate pairs. PeerJ. 2015;3:e996doi: 10.7717/peerj.996.
Murphy, R. R., O'Connell, J., Cox, A. J., & Schulz-Trieglaff, O. (2015). NxRepair: error correction in de novo sequence assembly using Nextera mate pairs. PeerJ, 3e996. https://doi.org/10.7717/peerj.996
Murphy, Rebecca R, et al. "NxRepair: error correction in de novo sequence assembly using Nextera mate pairs." PeerJ vol. 3 (2015): e996. doi: https://doi.org/10.7717/peerj.996
Murphy RR, O'Connell J, Cox AJ, Schulz-Trieglaff O. NxRepair: error correction in de novo sequence assembly using Nextera mate pairs. PeerJ. 2015 Jun 02;3:e996. doi: 10.7717/peerj.996. eCollection 2015. PMID: 26056623; PMCID: PMC4458127.
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PeerJ. 2015 Jun 02;3:e996. doi: 10.7717/peerj.996. eCollection 2015.

NxRepair: error correction in de novo sequence assembly using Nextera mate pairs.

PeerJ

Rebecca R Murphy, Jared O'Connell, Anthony J Cox, Ole Schulz-Trieglaff

Affiliations

  1. Department of Chemistry, University of Cambridge , UK.
  2. Illumina Cambridge, Chesterford Research Park , Essex , UK.

PMID: 26056623 PMCID: PMC4458127 DOI: 10.7717/peerj.996

Abstract

Scaffolding errors and incorrect repeat disambiguation during de novo assembly can result in large scale misassemblies in draft genomes. Nextera mate pair sequencing data provide additional information to resolve assembly ambiguities during scaffolding. Here, we introduce NxRepair, an open source toolkit for error correction in de novo assemblies that uses Nextera mate pair libraries to identify and correct large-scale errors. We show that NxRepair can identify and correct large scaffolding errors, without use of a reference sequence, resulting in quantitative improvements in the assembly quality. NxRepair can be downloaded from GitHub or PyPI, the Python Package Index; a tutorial and user documentation are also available.

Keywords: Assembly quality; Automated error detection; De novo assembly; Error correction; Genome assembly; Insert size; Mate pair; Misassembly; Misassembly detection; Scaffolding

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