SVIM-asm: structural variant detection from haploid and diploid genome assemblies.

ABSTRACT:

Motivation

With the availability of new sequencing technologies, the generation of haplotype-resolved genome assemblies up to chromosome scale has become feasible. These assemblies capture the complete genetic information of both parental haplotypes, increase structural variant (SV) calling sensitivity and enable direct genotyping and phasing of SVs. Yet, existing SV callers are designed for haploid genome assemblies only, do not support genotyping or detect only a limited set of SV classes.

Results

We introduce our method SVIM-asm for the detection and genotyping of six common classes of SVs from haploid and diploid genome assemblies. Compared against the only other existing SV caller for diploid assemblies, DipCall, SVIM-asm detects more SV classes and reached higher F1 sc

SUBMITTER: Heller D 

PROVIDER: S-EPMC8016491 | biostudies-literature | 2021 Apr

REPOSITORIES: biostudies-literature