MeCorS: Metagenome-enabled error correction of single cell sequencing reads

Journal Article · Tue Mar 15 00:00:00 EDT 2016 · Bioinformatics

DOI: https://doi.org/10.1093/bioinformatics/btw144 · OSTI ID:1342957

Bremges, Andreas ^[1]; Singer, Esther ^[2]; Woyke, Tanja ^[2]; Sczyrba, Alexander ^[3]

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1. Bielefeld Univ., Bielefeld (Germany); U.S. Dept. of Energy Joint Genome Institute, Walnut Creek, CA (United States); DOE Office of Scientific and Technical Information (OSTI)
2. U.S. Dept. of Energy Joint Genome Institute, Walnut Creek, CA (United States)
3. Bielefeld Univ., Bielefeld (Germany); U.S. Dept. of Energy Joint Genome Institute, Walnut Creek, CA (United States)

Here we present a new tool, MeCorS, to correct chimeric reads and sequencing errors in Illumina data generated from single amplified genomes (SAGs). It uses sequence information derived from accompanying metagenome sequencing to accurately correct errors in SAG reads, even from ultra-low coverage regions. In evaluations on real data, we show that MeCorS outperforms BayesHammer, the most widely used state-of-the-art approach. MeCorS performs particularly well in correcting chimeric reads, which greatly improves both accuracy and contiguity of de novo SAG assemblies.

• Research Organization: USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
• Sponsoring Organization: USDOE Office of Science (SC)
• Grant/Contract Number: AC02-05CH11231
• OSTI ID: 1342957
• Journal Information: Bioinformatics, Journal Name: Bioinformatics Journal Issue: 14 Vol. 32; ISSN 1367-4803
• Publisher: International Society for Computational Biology - Oxford University PressCopyright Statement
• Country of Publication: United States
• Language: English