ArticlePloS one2013
Coval: improving alignment quality and variant calling accuracy for next-generation sequencing data.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 40 papers.
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40 citing papers in PubMed.
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- Genetic characterization of a locus responsible for low pungency using EMS-induced mutants in Capsicum annuum L.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- Deploying QTL-seq rapid identification and separation of the major QTLs of tassel branch number for fine-mapping in advanced maize populations.Molecular breeding : new strategies in plant improvement · 2023Article
- Whole-genome sequencing based discovery of candidate genes and diagnostic markers for seed weight in groundnut.The plant genome · 2023Article
- Genetic testing in monogenic early-onset atrial fibrillation.European journal of human genetics : EJHG · 2023Article
- Detection of a major QTL and development of KASP markers for seed weight by combining QTL-seq, QTL-mapping and RNA-seq in peanut.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2022Article
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- Identification of single major QTL and candidate gene(s) governing hull-less seed trait in pumpkin.Frontiers in plant science · 2022Article
- Whole Exome-Sequencing of Pooled Genomic DNA Samples to Detect Quantitative Trait Loci in Esotropia and Exotropia of Strabismus in Japanese.Life (Basel, Switzerland) · 2021Article
- Combining QTL-seq and linkage mapping to uncover the genetic basis of single vs. paired spikelets in the advanced populations of two-ranked maize×teosinte.BMC plant biology · 2021Article
- SorghumGenes · 2021Article
- MutMap Approach Enables Rapid Identification of Candidate Genes and Development of Markers Associated With Early Flowering and Enhanced Seed Size in Chickpea (Frontiers in plant science · 2021Article
- Developmental Modulation of Root Cell Wall Architecture Confers Resistance to an Oomycete Pathogen.Current biology : CB · 2020Article
- Discovery of genomic regions and candidate genes for grain weight employing next generation sequencing based QTL-seq approach in rice (Oryza sativa L.).Molecular biology reports · 2020Article
- Whole-genome resequencing-based QTL-seq identified candidate genes and molecular markers for fresh seed dormancy in groundnut.Plant biotechnology journal · 2020Article
- Diploid genome differentiation conferred by RNA sequencing-based survey of genome-wide polymorphisms throughout homoeologous loci in Triticum and Aegilops.BMC genomics · 2020Article
- QTL-seq reveals genomic regions associated with spikelet fertility in response to a high temperature in rice (Oryza sativa L.).Plant cell reports · 2020Article
Corrections and comments
- Erratum issued
Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Accurate identification of DNA polymorphisms using next-generation sequencing technology is challenging because of a high rate of sequencing error and incorrect mapping of reads to reference genomes. Currently available short read aligners and DNA variant callers suffer from these problems. We developed the Coval software to improve the quality of short read alignments. Coval is designed to minimize the incidence of spurious alignment of short reads, by filtering mismatched reads that remained in alignments after local realignment and error correction of mismatched reads. The error correction is executed based on the base quality and allele frequency at the non-reference positions for an individual or pooled sample. We demonstrated the utility of Coval by applying it to simulated genomes and experimentally obtained short-read data of rice, nematode, and mouse. Moreover, we found an unexpectedly large number of incorrectly mapped reads in 'targeted' alignments, where the whole genome sequencing reads had been aligned to a local genomic segment, and showed that Coval effectively eliminated such spurious alignments. We conclude that Coval significantly improves the quality of short-read sequence alignments, thereby increasing the calling accuracy of currently available tools for SNP and indel identification. Coval is available at http://sourceforge.net/projects/coval105/.
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