Large indel detection in region-based phased diploid assemblies from linked-reads.

ABSTRACT:

Background

Linked-reads improve de novo assembly, haplotype phasing, structural variant (SV) detection, and other applications through highly-multiplexed genome partitioning and barcoding. Whole genome assembly and assembly-based variant detection based on linked-reads often require intensive computation costs and are not suitable for large population studies. Here we propose an efficient pipeline, RegionIndel, a region-based diploid assembly approach to characterize large indel SVs. This pipeline only focuses on target regions (50kb by default) to extract barcoded reads as input and then integrates a haplotyping algorithm and local assembly to generate phased diploid contiguous sequences (contigs). Finally, it detects variants in the contigs through a pairwise contig-to-reference

SUBMITTER: Luo C 

PROVIDER: S-EPMC11916464 | biostudies-literature | 2025 Mar

REPOSITORIES: biostudies-literature