HECIL: A Hybrid Error Correction Algorithm for Long Reads with Iterative Learning

Second-generation sequencing techniques generate short reads that can result in fragmented genome assemblies. Third-generation sequencing platforms mitigate this limitation by producing longer reads that span across complex and repetitive regions. Currently, the usefulness of such long reads is limited, however, because of high sequencing error rates. To exploit the full potential of these longer reads, it is imperative to correct the underlying errors. We propose HECIL--Hybrid Error Correction with Iterative Learning--a hybrid error correction framework that determines a correction policy for erroneous long reads, based on optimal combinations of decision weights obtained from short read alignments. We demonstrate that HECIL outperforms state-of-the-art error correction algorithms for an overwhelming majority of evaluation metrics on diverse real data sets including E. coli, S. cerevisiae, and the malaria vector mosquito A. funestus. We further improve the performance of HECIL by introducing an iterative learning paradigm that improves the correction policy at each iteration by incorporating knowledge gathered from previous iterations via confidence metrics assigned to prior corrections.\n\nAvailability and Implementationhttps://github.com/NDBL/HECIL\n\nContactsemrich@nd.edu