title: NxRepair: error correction in de novo sequence assembly using Nextera mate pairs.
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.
authors.affiliation: Department of Chemistry, University of Cambridge , UK.
authors.forename: Rebecca R
authors.initials: RR
authors.lastname: Murphy
authors.affiliation: Illumina Cambridge, Chesterford Research Park , Essex , UK.
authors.forename: Jared
authors.initials: J
authors.lastname: O'Connell
authors.affiliation: Illumina Cambridge, Chesterford Research Park , Essex , UK.
authors.forename: Anthony J
authors.initials: AJ
authors.lastname: Cox
authors.affiliation: Illumina Cambridge, Chesterford Research Park , Essex , UK.
authors.forename: Ole
authors.initials: O
authors.lastname: Schulz-Trieglaff
keywords: Assembly quality; Automated error detection; De novo assembly; Error correction; Genome assembly; Insert size; Mate pair; Misassembly; Misassembly detection; Scaffolding