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This article is part of the supplement: Selected articles from the Eleventh Asia Pacific Bioinformatics Conference (APBC 2013): Genomics

Open Access Proceedings

BayesHammer: Bayesian clustering for error correction in single-cell sequencing

Sergey I Nikolenko1*, Anton I Korobeynikov12 and Max A Alekseyev13

Author affiliations

1 Algorithmic Biology Laboratory, Academic University, St. Petersburg, Russia

2 St. Petersburg State University, Russia

3 Department of Computer Science and Engineering, University of South Carolina, Columbia, SC, USA

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Citation and License

BMC Genomics 2013, 14(Suppl 1):S7  doi:10.1186/1471-2164-14-S1-S7

Published: 21 January 2013

Abstract

Error correction of sequenced reads remains a difficult task, especially in single-cell sequencing projects with extremely non-uniform coverage. While existing error correction tools designed for standard (multi-cell) sequencing data usually come up short in single-cell sequencing projects, algorithms actually used for single-cell error correction have been so far very simplistic.

We introduce several novel algorithms based on Hamming graphs and Bayesian subclustering in our new error correction tool BAYESHAMMER. While BAYESHAMMER was designed for single-cell sequencing, we demonstrate that it also improves on existing error correction tools for multi-cell sequencing data while working much faster on real-life datasets. We benchmark BAYESHAMMER on both k-mer counts and actual assembly results with the SPADES genome assembler.