ArticlePloS one2017
Evaluating alignment and variant-calling software for mutation identification in C. elegans by whole-genome sequencing.
Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed.
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- A complement factor H homolog, heparan sulfation, and syndecan maintain inversin compartment boundaries inProceedings of the National Academy of Sciences of the United States of America · 2021Article
- Harnessing the power of genetics: fast forward genetics in Caenorhabditis elegans.Molecular genetics and genomics : MGG · 2021Review
- Transformation of nonencapsulated Streptococcus pneumoniae during systemic infection.Scientific reports · 2020Article
- Identification of Suppressors ofG3 (Bethesda, Md.) · 2020Article
- Toc75-V/OEP80 is processed during translocation into chloroplasts, and the membrane-embedded form exposes its POTRA domain to the intermembrane space.FEBS open bio · 2020Article
- Genomic diversity affects the accuracy of bacterial single-nucleotide polymorphism-calling pipelines.GigaScience · 2020Article
- DNAscan: personal computer compatible NGS analysis, annotation and visualisation.BMC bioinformatics · 2019Article
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2 authors.
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Abstract
Whole-genome sequencing is a powerful tool for analyzing genetic variation on a global scale. One particularly useful application is the identification of mutations obtained by classical phenotypic screens in model species. Sequence data from the mutant strain is aligned to the reference genome, and then variants are called to generate a list of candidate alleles. A number of software pipelines for mutation identification have been targeted to C. elegans, with particular emphasis on ease of use, incorporation of mapping strain data, subtraction of background variants, and similar criteria. Although success is predicated upon the sensitive and accurate detection of candidate alleles, relatively little effort has been invested in evaluating the underlying software components that are required for mutation identification. Therefore, we have benchmarked a number of commonly used tools for sequence alignment and variant calling, in all pair-wise combinations, against both simulated and actual datasets. We compared the accuracy of those pipelines for mutation identification in C. elegans, and found that the combination of BBMap for alignment plus FreeBayes for variant calling offers the most robust performance.
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