Identification of errors in draft genome assemblies at single-nucleotide resolution for quality assessment and improvement.

ABSTRACT: Assembly of a high-quality genome is important for downstream comparative and functional genomic studies. However, most tools for genome assembly assessment only give qualitative reports, which do not pinpoint assembly errors at specific regions. Here, we develop a new reference-free tool, Clipping information for Revealing Assembly Quality (CRAQ), which maps raw reads back to assembled sequences to identify regional and structural assembly errors based on effective clipped alignment information. Error counts are transformed into corresponding assembly evaluation indexes to reflect the assembly quality at single-nucleotide resolution. Notably, CRAQ distinguishes assembly errors from heterozygous sites or structural differences between haplotypes. This tool can clearly indicate low-quality

SUBMITTER: Li K 

PROVIDER: S-EPMC10582259 | biostudies-literature | 2023 Oct

REPOSITORIES: biostudies-literature