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

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.