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

    loading  Checking for direct PDF access through Ovid

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.

    loading  Loading Related Articles