Overcoming uncollapsed haplotypes in long-read assemblies of non-model organisms.

ABSTRACT:

Background

Long-read sequencing is revolutionizing genome assembly: as PacBio and Nanopore technologies become more accessible in technicity and in cost, long-read assemblers flourish and are starting to deliver chromosome-level assemblies. However, these long reads are usually error-prone, making the generation of a haploid reference out of a diploid genome a difficult enterprise. Failure to properly collapse haplotypes results in fragmented and structurally incorrect assemblies and wreaks havoc on orthology inference pipelines, yet this serious issue is rarely acknowledged and dealt with in genomic projects, and an independent, comparative benchmark of the capacity of assemblers and post-processing tools to properly collapse or purge haplotypes is still lacking.

Results

We

SUBMITTER: Guiglielmoni N 

PROVIDER: S-EPMC8178825 | biostudies-literature | 2021 Jun

REPOSITORIES: biostudies-literature