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Identification of errors in draft genome assemblies at single-nucleotide resolution for quality assessment and improvement
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Identification of errors in draft genome assemblies at single-nucleotide resolution for quality assessment and improvement
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Identification of errors in draft genome assemblies at single-nucleotide resolution for quality assessment and improvement
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Journal Article
Identification of errors in draft genome assemblies at single-nucleotide resolution for quality assessment and improvement
2023
Overview
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 regions and potential structural error breakpoints; thus, it can identify misjoined regions that should be split for further scaffold building and improvement of the assembly. We have benchmarked CRAQ on multiple genomes assembled using different strategies, and demonstrated the misjoin correction for improving the constructed pseudomolecules.
A high-quality genome assembly is essential for various genomic studies in life sciences. Here the authors develop CRAQ, a reference-free method that facilitates the evaluation and improvement of any de novo genome assembly with single nucleotide resolution.
Publisher
Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
Subject
