Identifying and removing haplotypic duplication in primary genome assemblies.

ABSTRACT:

Motivation

Rapid development in long-read sequencing and scaffolding technologies is accelerating the production of reference-quality assemblies for large eukaryotic genomes. However, haplotype divergence in regions of high heterozygosity often results in assemblers creating two copies rather than one copy of a region, leading to breaks in contiguity and compromising downstream steps such as gene annotation. Several tools have been developed to resolve this problem. However, they either focus only on removing contained duplicate regions, also known as haplotigs, or fail to use all the relevant information and hence make errors.

Results

Here we present a novel tool, purge_dups, that uses sequence similarity and read depth to automatically identify and remove both haplotigs an

SUBMITTER: Guan D 

PROVIDER: S-EPMC7203741 | biostudies-literature | 2020 May

REPOSITORIES: biostudies-literature