ArticleNature communications2023
Identification of errors in draft genome assemblies at single-nucleotide resolution for quality assessment and improvement.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 83 papers.
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Who cites it
83 citing papers in PubMed.
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- Assembly-graph-assisted haplotype-resolved scaffolding of polyploid genomes.Nature plants · 2026Article
- Pan-genomics and multi-omics for deciphering genetic variation and accelerating genetic improvement in ruminant livestock.Functional & integrative genomics · 2026Review
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- Near telomere-to-telomere genome assembly of the rainbow trout (Oncorhynchus mykiss).Scientific data · 2026Article
- theBIGbam: compression and interactive exploration of large-scale sequencing alignments with circular mapping support.Bioinformatics (Oxford, England) · 2026Article
- Chromosome-scale Genome Assembly and Annotation of Anise Hyssop (Agastache foeniculum).Scientific data · 2026Article
- ChromoMapperWeb: evaluate genome alignments and track assembly steps within an interactive graphic environment.Nucleic acids research · 2026Article
- A dual genome-methylome map of clonal evolution in grapevine.Genome biology · 2026Article
- MGA: a tool for haplotype-mixed assembly of long and accurate reads.Genome biology · 2026Article
- A Near Telomere-to-Telomere Genome of Belamcanda chinensis Provides Insights Into Genome Evolution and the Biosynthesis of Characteristic Isoflavones.Plant biotechnology journal · 2026Article
- From contiguity to accuracy: Validation-centered perspectives on bacterial genome assembly.Journal of microbiology (Seoul, Korea) · 2026Review
- Genome analysis of Channel millet reveals a wild dodecaploid shaped by environmental variability.Nature communications · 2026Article
- High-Contiguity Haplotype-Resolved Genome Assembly of the Hexaploid Actinidia valvata Rootstock Sheds Light on Waterlogging Resistance Gene.Plant biotechnology journal · 2026Article
- Pan-genome analysis uncovers extensive structural variations in Africa's indigenous legume crop cowpea.Nature communications · 2026Article
- PAQman: reference-free ensemble evaluation of long-read genome assemblies.G3 (Bethesda, Md.) · 2026Article
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- Transposable Element-Mediated Structural Variation Drives Flower Colour Diversification in Camellia.Plant biotechnology journal · 2026Article
23 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
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 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.
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