ArticlePlants (Basel, Switzerland)2020
Comparison of Read Mapping and Variant Calling Tools for the Analysis of Plant NGS Data.
Article in Plants (Basel, Switzerland), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- Genomic structural variation rescues a classic biological invader from a population bottleneck.Science advances · 2026Article
- Bridging tradition and innovation: a review of computer simulations in plant breeding.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Review
- Accurate detections of the heterozygous SNPs with rice genomic data and prediction of de novo spontaneous mutation rate.Plant methods · 2025Article
- Benchmarking of low coverage sequencing workflows for precision genotyping in eggplant.BMC plant biology · 2025Article
- NewtCap: An Efficient Target Capture Approach to Boost Genomic Studies in Salamandridae (True Salamanders and Newts).Ecology and evolution · 2025Article
- A reproducible ddRAD-seq protocol reveals novel genomic association signatures for fruit-related traits in peach.Plant methods · 2025Article
- A comprehensive catalog of single nucleotide polymorphisms (SNPs) from the black pepper (Piper nigrum L.) genome.BMC genomics · 2025Article
- NAVIP: Unraveling the influence of neighboring small sequence variants on functional impact prediction.PLoS computational biology · 2025Article
- Development and validation of a minimal SNP genotyping panel for the differentiation of Cannabis sativa cultivars.BMC genomics · 2025Article
- High-throughput method characterizes hundreds of previously unknown antibiotic resistance mutations.Nature communications · 2025Article
- An in vitro approach reveals molecular mechanisms underlying endocrine disruptor-induced epimutagenesis.eLife · 2024Article
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- Data literacy in genome research.Journal of integrative bioinformatics · 2023Review
- Short-read aligner performance in germline variant identification.Bioinformatics (Oxford, England) · 2023Review
- Evaluation of variant calling algorithms for wastewater-based epidemiology using mixed populations of SARS-CoV-2 variants in synthetic and wastewater samples.Microbial genomics · 2023Article
- Differential Expression of miRNAs Involved in Response toPlants (Basel, Switzerland) · 2023Article
- From Classical to Modern Computational Approaches to Identify Key Genetic Regulatory Components in Plant Biology.International journal of molecular sciences · 2023Review
- Accelerating the alignment processing speed of the comprehensive end-to-end whole-genome bisulfite sequencing pipeline, wg-blimp.Biology methods & protocols · 2023Article
- Ultra-high static magnetic field induces a change in the spectrum but not frequency of DNA spontaneous mutations inFrontiers in plant science · 2023Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
High-throughput sequencing technologies have rapidly developed during the past years and have become an essential tool in plant sciences. However, the analysis of genomic data remains challenging and relies mostly on the performance of automatic pipelines. Frequently applied pipelines involve the alignment of sequence reads against a reference sequence and the identification of sequence variants. Since most benchmarking studies of bioinformatics tools for this purpose have been conducted on human datasets, there is a lack of benchmarking studies in plant sciences. In this study, we evaluated the performance of 50 different variant calling pipelines, including five read mappers and ten variant callers, on six real plant datasets of the model organism
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