Population-scale detection of non-reference sequence variants using colored de Bruijn graphs.

ABSTRACT:

Motivation

With the increasing throughput of sequencing technologies, structural variant (SV) detection has become possible across tens of thousands of genomes. Non-reference sequence (NRS) variants have drawn less attention compared with other types of SVs due to the computational complexity of detecting them. When using short-read data, the detection of NRS variants inevitably involves a de novo assembly which requires high-quality sequence data at high coverage. Previous studies have demonstrated how sequence data of multiple genomes can be combined for the reliable detection of NRS variants. However, the algorithms proposed in these studies have limited scalability to larger sets of genomes.

Results

We introduce PopIns2, a tool to discover and characterize NRS variants i

SUBMITTER: Krannich T 

PROVIDER: S-EPMC8756200 | biostudies-literature | 2022 Jan

REPOSITORIES: biostudies-literature