ArticlePloS one2025
Fast and accurate imputation of genotypes from noisy low-coverage sequencing data in bi-parental populations.
Article in PloS one, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- Skim-sequencing for genomic selection in wheat: a comparison of marker platforms.The plant genome · 2026Article
- dCas9-SPO11-1 locally stimulates meiotic recombination in rice.Frontiers in plant science · 2025Article
- Utilization of Genotyping-by-Sequencing (GBS) for Rice Pre-Breeding and Improvement: A Review.Life (Basel, Switzerland) · 2022Review
- Genotype imputation for soybean nested association mapping population to improve precision of QTL detection.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2022Article
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationGenotyping of bi-parental populations can be performed with low-coverage next-generation sequencing (LC-NGS). This allows the creation of highly saturated genetic maps at reasonable cost, precisely localized recombination breakpoints (i.e., the crossovers), and minimized mapping intervals for quantitative-trait locus analysis. The main issues with these low-coverage genotyping methods are (1) poor performance at heterozygous loci, (2) high percentage of missing data, (3) local errors due to erroneous mapping of sequencing reads and reference genome mistakes, and (4) global, technical errors inherent to NGS itself. Recent methods like Tassel-FSFHap or LB-Impute are excellent at addressing issues 1 and 2, but nonetheless perform poorly when issues 3 and 4 are persistent in a dataset (i.e., "noisy" data). Here, we present a new algorithm for imputation of LC-NGS data that eliminates the need of complex pre-filtering of noisy data, accurately types heterozygous chromosomal regions, precisely estimates crossover positions, corrects erroneous data, and imputes missing data. The imputation of genotypes and recombination breakpoints is based on maximum-likelihood estimation. We compare its performance with Tassel-FSFHap and LB-Impute using simulated data and two real datasets. NOISYmputer is consistently more efficient than the two other software tested and reaches average breakpoint precision of 99.9% and average recall of 99.6% on illumina simulated dataset. NOISYmputer consistently provides precise map size estimations when applied to real datasets while alternative tools may exhibit errors ranging from 3 to 1845 times the real size of the chromosomes in centimorgans. Furthermore, the algorithm is not only highly effective in terms of precision and recall but is also particularly economical in its use of RAM and computation time, being much faster than Hidden Markov Model methods. AVAILABILITY: NOISYmputer and its source code are available as a multiplatform (Linux, macOS, Windows) Java executable at the URL https://gitlab.cirad.fr/noisymputer/noisymputerstandalone/-/tree/1.0.0-RELEASE?reftype=tags.
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