期刊
PEERJ
卷 3, 期 -, 页码 -出版社
PEERJ INC
DOI: 10.7717/peerj.996
关键词
De novo assembly; Mate pair; Genome assembly; Error correction; Scaffolding; Insert size; Misassembly; Misassembly detection; Assembly quality; Automated error detection
资金
- Biotechnology and Biological Sciences Research Council [1127851] Funding Source: researchfish
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 fromGitHub or PyPI, the Python Package Index; a tutorial and user documentation are also available.
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