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

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.cn. Supplementary information: Supplementary data are available at Bioinformatics online.