ArticleBMC genomics2018
Mining statistically-solid k-mers for accurate NGS error correction.
Article in BMC genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Fine mapping and candidate gene analysis of qPH19.1, a locus for soybean (Glycine max L.) plant height.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- K-mer-based Approaches to Bridging Pangenomics and Population Genetics.Molecular biology and evolution · 2025Review
- Role of F-box E3-ubiquitin ligases in plant development and stress responses.Plant cell reports · 2023Review
- Comprehensive investigation of long non-coding RNAs in an endophytic fungus Calcarisporium arbuscula NRRL 3705.Archives of microbiology · 2023Article
- Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2.Genome biology · 2022Article
- Gene Mining and Flavour Metabolism Analyses ofFrontiers in microbiology · 2022Article
- The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms.F1000Research · 2022Article
- Comparative analysis of 7 short-read sequencing platforms using the Korean Reference Genome: MGI and Illumina sequencing benchmark for whole-genome sequencing.GigaScience · 2021Article
- Dual UMIs and Dual Barcodes With Minimal PCR Amplification Removes Artifacts and Acquires Accurate Antibody Repertoire.Frontiers in immunology · 2021Article
- Efficient Mining of Variants From Trios for Ventricular Septal Defect Association Study.Frontiers in genetics · 2019Article
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundNGS data contains many machine-induced errors. The most advanced methods for the error correction heavily depend on the selection of solid k-mers. A solid k-mer is a k-mer frequently occurring in NGS reads. The other k-mers are called weak k-mers. A solid k-mer does not likely contain errors, while a weak k-mer most likely contains errors. An intensively investigated problem is to find a good frequency cutoff f
resultsWe propose to use a Gamma distribution to model the frequencies of erroneous k-mers and a mixture of Gaussian distributions to model correct k-mers, and combine them to determine f
conclusionThe z-score is adequate to distinguish solid k-mers from weak k-mers, particularly useful for pinpointing out solid k-mers having very low frequency. Applying z-score on k-mer can markedly improve the error correction accuracy.
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