NucBreak: location of structural errors in a genome assembly by using paired-end Illumina reads.

ABSTRACT: BACKGROUND:Advances in whole genome sequencing strategies have provided the opportunity for genomic and comparative genomic analysis of a vast variety of organisms. The analysis results are highly dependent on the quality of the genome assemblies used. Assessment of the assembly accuracy may significantly increase the reliability of the analysis results and is therefore of great importance. RESULTS:Here, we present a new tool called NucBreak aimed at localizing structural errors in assemblies, including insertions, deletions, duplications, inversions, and different inter- and intra-chromosomal rearrangements. The approach taken by existing alternative tools is based on analysing reads that do not map properly to the assembly, for instance discordantly mapped reads, soft-clipped reads and s

SUBMITTER: Khelik K 

PROVIDER: S-EPMC7035700 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature