PREMIER — PRobabilistic error-correction using Markov inference in errored reads

In this work we present a flexible, probabilistic and reference-free method of error correction for high throughput DNA sequencing data. The key is to exploit the high coverage of sequencing data and model short sequence outputs as independent realizations of a Hidden Markov Model (HMM). We pose the problem of error correction of reads as one of maximum likelihood sequence detection over this HMM. While time and memory considerations rule out an implementation of the optimal Baum-Welch algorithm (for parameter estimation) and the optimal Viterbi algorithm (for error correction), we propose low-complexity approximate versions of both. Specifically, we propose an approximate Viterbi and a sequential decoding based algorithm for the error correction. Our results show that when compared with Reptile, a state-of-the-art error correction method, our methods consistently achieve superior performances on both simulated and real data sets.