The DOI matches its Crossref record; 9 of the 9 references it cites were found in a registry or an index.
KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies
Open accessAbstract
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. Supplementary information: Supplementary data are available at Bioinformatics online.
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Cited by
Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies
Rhie, A., Walenz, B. P., Koren, S., & Phillippy, A. M. (2020) · Genome Biology · doi:10.1186/s13059-020-02134-9 · Cited by 3,643
Towards complete and error-free genome assemblies of all vertebrate species
Rhie, A., McCarthy, S. A., Fedrigo, O., Damas, J., Formenti, G., Koren, S., Uliano-Silva, M., Chow, W., Fungtammasan, A., Kim, J., et al. (2021) · Nature · doi:10.1038/s41586-021-03451-0 · Cited by 3,097
Towards complete and error-free genome assemblies of all vertebrate species
Rhie, A., McCarthy, S. A., Fedrigo, O., Damas, J., Formenti, G., Koren, S., Uliano-Silva, M., Chow, W., Fungtammasan, A., Gedman, G. L., et al. (2020) · doi:10.1101/2020.05.22.110833 · Cited by 3,097
Identifying and removing haplotypic duplication in primary genome assemblies
Guan, D., McCarthy, S. A., Wood, J., Howe, K., Wang, Y., & Durbin, R. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btaa025 · Cited by 2,706
Significantly improving the quality of genome assemblies through curation
Howe, K., Chow, W., Collins, J., Pelan, S., Pointon, D.-L., Sims, Y., Torrance, J., Tracey, A., & Wood, J. (2021) · GigaScience · doi:10.1093/gigascience/giaa153 · Cited by 2,090
Metadata
- Authors
- Mapleson, D., Garcia Accinelli, G., Kettleborough, G., Wright, J., & Clavijo, B. J.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2016-11-28
- Volume
- 33
- Issue
- 4
- Pages
- 574-576
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2952136406
- Cited by
- 538
- References
- 9
- FWCI
- 9.93
- Type
- journal article
- Language
- en
- Open access
- hybrid
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