PECC: Correcting contigs based on paired-end read distribution. (August 2017)
- Record Type:
- Journal Article
- Title:
- PECC: Correcting contigs based on paired-end read distribution. (August 2017)
- Main Title:
- PECC: Correcting contigs based on paired-end read distribution
- Authors:
- Li, Min
Wu, Binbin
Yan, Xiaodong
Luo, Junwei
Pan, Yi
Wu, Fang-Xiang
Wang, Jianxin - Abstract:
- Abstract: Motivation: Cheap and fast next generation sequencing (NGS) technologies facilitate research of de novo assembly greatly. The reliability of contigs is critical to construct reliable scaffolding. However, contigs generated from most assemblers contain errors because of the limitation of assembly strategy and computation complexity. Among all these errors, the misassembly error is one of the most harmful types. Results: In this paper, we propose a new method named "PECC" to identify and correct misassembly errors in contigs based on the paired-end read distribution. PECC extracts sequence regions with lower paired-end reads supports and verifies them based on the distribution of paired-end supports. To validate the effectiveness of PECC, we applied PECC to the contigs produced by five popular assemblers on four real datasets, and we also carried out experiments to analyze the influences of PECC on scaffolding. The results show that PECC can reduce misassembly errors and improve the performance of scaffolding results, which demonstrate the promising applications of PECC in de novo assembly.
- Is Part Of:
- Computational biology and chemistry. Volume 69(2017)
- Journal:
- Computational biology and chemistry
- Issue:
- Volume 69(2017)
- Issue Display:
- Volume 69, Issue 2017 (2017)
- Year:
- 2017
- Volume:
- 69
- Issue:
- 2017
- Issue Sort Value:
- 2017-0069-2017-0000
- Page Start:
- 178
- Page End:
- 184
- Publication Date:
- 2017-08
- Subjects:
- Next generation sequencing -- De novo assembly -- Contigs -- Paired-end reads
Chemistry -- Data processing -- Periodicals
Biology -- Data processing -- Periodicals
Biochemistry -- Data processing
Biology -- Data processing
Molecular biology -- Data processing
Periodicals
Electronic journals
542.85 - Journal URLs:
- http://www.sciencedirect.com/science/journal/14769271 ↗
http://www.elsevier.com/journals ↗ - DOI:
- 10.1016/j.compbiolchem.2017.03.012 ↗
- Languages:
- English
- ISSNs:
- 1476-9271
- Deposit Type:
- Legaldeposit
- View Content:
- Available online (eLD content is only available in our Reading Rooms) ↗
- Physical Locations:
- British Library DSC - 3390.576700
British Library DSC - BLDSS-3PM
British Library STI - ELD Digital store - Ingest File:
- 2928.xml