Error correcting optical mapping data

GigaScience
Kingshuk MukherjeeChristina Boucher

Abstract

Optical mapping is a unique system that is capable of producing high-resolution, high-throughput genomic map data that gives information about the structure of a genome . Recently it has been used for scaffolding contigs and for assembly validation for large-scale sequencing projects, including the maize, goat, and Amborella genomes. However, a major impediment in the use of this data is the variety and quantity of errors in the raw optical mapping data, which are called Rmaps. The challenges associated with using Rmap data are analogous to dealing with insertions and deletions in the alignment of long reads. Moreover, they are arguably harder to tackle since the data are numerical and susceptible to inaccuracy. We develop cOMet to error correct Rmap data, which to the best of our knowledge is the only optical mapping error correction method. Our experimental results demonstrate that cOMet has high prevision and corrects 82.49% of insertion errors and 77.38% of deletion errors in Rmap data generated from the Escherichia coli K-12 reference genome. Out of the deletion errors corrected, 98.26% are true errors. Similarly, out of the insertion errors corrected, 82.19% are true errors. It also successfully scales to large genomes, i...Continue Reading

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Citations

Jan 31, 2019·Bioinformatics·Kingshuk MukherjeeChristina Boucher
Sep 11, 2019·Bioinformatics·Leena SalmelaChristina Boucher
Aug 18, 2020·Computational and Structural Biotechnology Journal·Yuxuan YuanTing-Fung Chan
May 14, 2021·Bioinformatics·Michal VašinekEva Kriegová
May 27, 2021·Algorithms for Molecular Biology : AMB·Kingshuk MukherjeeChristina Boucher

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