ArticleBioinformatics (Oxford, England)2017
KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies.
Article in Bioinformatics (Oxford, England), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 323 papers.
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323 citing papers in PubMed.
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- Whole genome sequencing of historical specimens from the world's largest fungal collection yields high-quality assemblies.The New phytologist · 2026Article
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- Convergence and divergence of DNA methylation and gene expression patterns in neopolyploid Arabidopsis kamchatica.Nature communications · 2026Article
- Wild tomato genome assemblies reveal structural variants and repeat content act as recombination barriers.Nature communications · 2026Article
- From contiguity to accuracy: Validation-centered perspectives on bacterial genome assembly.Journal of microbiology (Seoul, Korea) · 2026Review
- A chromosome-level genome for gila trout (Oncorhynchus gilae) provides a novel resource for conservation and management.BMC genomics · 2026Article
- A chromosome-level genome assembly of Vanilla planifolia uncovers the genomic architecture underlying partial endoreplication.BMC genomics · 2026Article
- High-quality genome and transcriptome resources for the East Asian freshwater mussel Nodularia douglasiae.Scientific data · 2026Article
- Pangenomic analyses of rose uncover widespread structure variation and empower genomics-directed breeding.Nature genetics · 2026Article
- Diploid chromosome-level genome assembly of the Amazonian endemic morning glory Ipomoea cavalcantei D.F. Austin.Scientific data · 2026Article
263 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
Funding
Abstract
Motivation: De novo assembly of whole genome shotgun (WGS) next-generation sequencing (NGS) data benefits from high-quality input with high coverage. However, in practice, determining the quality and quantity of useful reads quickly and in a reference-free manner is not trivial. Gaining a better understanding of the WGS data, and how that data is utilized by assemblers, provides useful insights that can inform the assembly process and result in better assemblies. Results: We present the K-mer Analysis Toolkit (KAT): a multi-purpose software toolkit for reference-free quality control (QC) of WGS reads and de novo genome assemblies, primarily via their k-mer frequencies and GC composition. KAT enables users to assess levels of errors, bias and contamination at various stages of the assembly process. In this paper we highlight KAT's ability to provide valuable insights into assembly composition and quality of genome assemblies through pairwise comparison of k-mers present in both input reads and the assemblies. Availability and Implementation: KAT is available under the GPLv3 license at: https://github.com/TGAC/KAT . Contact: bernardo.clavijo@earlham.ac.uk. Supplementary information: Supplementary data are available at Bioinformatics online.
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