Evaluating Illumina-, Nanopore-, and PacBio-based genome assembly strategies with the bald notothen, Trematomus borchgrevinki.

ABSTRACT: For any genome-based research, a robust genome assembly is required. De novo assembly strategies have evolved with changes in DNA sequencing technologies and have been through at least 3 phases: (1) short-read only, (2) short- and long-read hybrid, and (3) long-read only assemblies. Each of the phases has its own error model. We hypothesized that hidden short-read scaffolding errors and erroneous long-read contigs degrade the quality of short- and long-read hybrid assemblies. We assembled the genome of Trematomus borchgrevinki from data generated during each of the 3 phases and assessed the quality problems we encountered. We developed strategies such as k-mer-assembled region replacement, parameter optimization, and long-read sampling to address the error models. We demonstrated that a k-

SUBMITTER: Rayamajhi N 

PROVIDER: S-EPMC9635638 | biostudies-literature | 2022 Nov

REPOSITORIES: biostudies-literature