How error correction affects polymerase chain reaction deduplication: A survey based on unique molecular identifier datasets of short reads

Abstract

Next-generation sequencing data are widely utilised for various downstream applications in bioinformatics and numerous techniques have been developed for PCR-deduplication and error-correction to eliminate bias and errors introduced during the sequencing. This study first-time provides a joint overview of recent advances in PCR-deduplication and error-correction on short reads. In particular, we utilise UMI-based PCR-deduplication strategies and sequencing data to assess the performance of the solely-computational PCR-deduplication approaches and investigate how error correction affects the performance of PCR-deduplication. Our survey and comparative analysis reveal that the deduplicated reads generated by the solely-computational PCR-deduplication and error-correction methods exhibit substantial differences and divergence from the sets of reads obtained by the UMI-based deduplication methods. The existing solely-computational PCR-deduplication and error-correction tools can eliminate some errors but still leave hundreds of thousands of erroneous reads uncorrected. All the error-correction approaches raise thousands or more new sequences after correction which do not have any benefit to the PCR-deduplication process. Based on our findings, we discuss future research directions and make suggestions for improving existing computational approaches to enhance the quality of short-read sequencing data.

Keywords

error correction / next generation sequencing (NGS) / PCR-deduplication / polymerase chain reaction (PCR) duplicates / unique molecular identifier (UMI)

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The Author(s). Quantitative Biology published by John Wiley & Sons Australia, Ltd on behalf of Higher Education Press.