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Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
Published on: June 23, 2012
rMFilter: acceleration of long read-based structure variation calling by chimeric read filtering
1Center for Bioinformatics, School of Computer Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China.
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.
