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Presented By: DCMB Tools and Technology Seminar

DCM&B Tools and Technology Seminar

Tim Dunn, “nPoRe: n-Polymer Realigner for improved pileup variant calling”

npore is a read realigner which recalculates each read's fine-grained alignment in order to more accurately align ''n-polymers'' such as homopolymers (n=1) and tandem repeats (2 ≤ n ≤ 6). In other words, given an input BAM, it adjusts each read's CIGAR string to more accurately model the most likely sequencing errors and actual variants. Traditional affine gap penalties are context-agnostic, and do not model the higher likelihood of INDELs in low-complexity regions (particularly n-polymers), leading to poor or inconsistent alignments. We find that npore improves pileup concordance across reads and results in slightly better variant calling performance.

Tool Link: https://github.com/TimD1/nPoRe

This presentation will be held in 2036 Palmer Commons. There will also be a remote viewing option via Zoom.

Livestream Information

 Livestream
September 15, 2022 (Thursday) 12:00pm

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