Combining probabilistic alignments with read pair information improves accuracy of split-alignments.

ABSTRACT:

Motivation

Split-alignments provide base-pair-resolution evidence of genomic rearrangements. In practice, they are found by first computing high-scoring local alignments, parts of which are then combined into a split-alignment. This approach is challenging when aligning a short read to a large and repetitive reference, as it tends to produce many spurious local alignments leading to ambiguities in identifying the correct split-alignment. This problem is further exacerbated by the fact that rearrangements tend to occur in repeat-rich regions.

Results

We propose a split-alignment technique that combats the issue of ambiguous alignments by combining information from probabilistic alignment with positional information from paired-end reads. We demonstrate that our method finds a

SUBMITTER: Shrestha AMS 

PROVIDER: S-EPMC6198854 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature