rMFilter: acceleration of long read-based structure variation calling by chimeric read filtering


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Abstract

Motivation:Long read sequencing technologies provide new opportunities to investigate genome structural variations (SVs) more accurately. However, the state-of-the-art SV calling pipelines are computational intensive and the applications of long reads are restricted.Results:We propose a local region match-based filter (rMFilter) to efficiently nail down chimeric noisy long reads based on short token matches within local genomic regions. rMFilter is able to substantially accelerate long read-based SV calling pipelines without loss of effectiveness. It can be easily integrated into current long read-based pipelines to facilitate SV studies.Availability and implementation:The C ++ source code of rMFilter is available at https://github.com/hitbc/rMFilter.Contact:ydwang@hit.edu.cnSupplementary information:Supplementary data are available at Bioinformatics online.

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