Fast and accurate correction of optical mapping data via spaced seeds | Zendy

Leena Salmela | Zendy; Kingshuk Mukherjee | Zendy; Simon J. Puglisi | Zendy; Martin D. Muggli | Zendy; Christina Boucher | Zendy

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Fast and accurate correction of optical mapping data via spaced seeds

Author(s) -

Leena Salmela,

Kingshuk Mukherjee,

Simon J. Puglisi,

Martin D. Muggli,

Christina Boucher

Publication year - 2019

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btz663

Subject(s) - computer science , spurious relationship , contig , error detection and correction , context (archaeology) , comet , sequence assembly , algorithm , genome , data mining , biology , genetics , physics , astrophysics , machine learning , paleontology , gene expression , transcriptome , gene

Optical mapping data is used in many core genomics applications, including structural variation detection, scaffolding assembled contigs and mis-assembly detection. However, the pervasiveness of spurious and deleted cut sites in the raw data, which are called Rmaps, make assembly and alignment of them challenging. Although there exists another method to error correct Rmap data, named cOMet, it is unable to scale to even moderately large sized genomes. The challenge faced in error correction is in determining pairs of Rmaps that originate from the same region of the same genome.

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