ArticleScientific reports2017
Direct comparison of performance of single nucleotide variant calling in human genome with alignment-based and assembly-based approaches.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers, 1 of them a synthesis that pooled it.
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Who cites it
11 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Vertical lossless genomic data compression tools for assembled genomes: A systematic literature review.PloS one · 2020Pooled it
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- A new long-read mitochondrial-genome protocol (PacBio HiFi) for haemosporidian parasites: a tool for population and biodiversity studies.Malaria journal · 2024Article
- Reversible gene silencing through frameshift indels and frameshift scars provide adaptive plasticity for Mycobacterium tuberculosis.Nature communications · 2021Article
- A Bioinformatics Whole-Genome Sequencing Workflow for Clinical Mycobacterium tuberculosis Complex Isolate Analysis, Validated Using a Reference Collection Extensively Characterized with Conventional Methods andJournal of clinical microbiology · 2021Article
- Aquila enables reference-assisted diploid personal genome assembly and comprehensive variant detection based on linked reads.Nature communications · 2021Article
- Genome-Wide Analysis of Nubian Ibex Reveals Candidate Positively Selected Genes That Contribute to Its Adaptation to the Desert Environment.Animals : an open access journal from MDPI · 2020Article
- On Variant Discovery in Genomes of Fungal Plant Pathogens.Frontiers in microbiology · 2020Article
- Fast-Seq: A Simple Method for Rapid and Inexpensive Validation of Packaged Single-Stranded Adeno-Associated Viral Genomes in Academic Settings.Human gene therapy methods · 2019Article
- Rare variants in the neuronal ceroid lipofuscinosis gene MFSD8 are candidate risk factors for frontotemporal dementia.Acta neuropathologica · 2019Article
- Pan-Genomic and Polymorphic Driven Prediction of Antibiotic Resistance inFrontiers in microbiology · 2019Article
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Authors and funding
5 authors.
Funding
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Abstract
Complementary to reference-based variant detection, recent studies revealed that many novel variants could be detected with de novo assembled genomes. To evaluate the effect of reads coverage and the accuracy of assembly-based variant calling, we simulated short reads containing more than 3 million of single nucleotide variants (SNVs) from the whole human genome and compared the efficiency of SNV calling between the assembly-based and alignment-based calling approaches. We assessed the quality of the assembled contig and found that a minimum of 30X coverage of short reads was needed to ensure reliable SNV calling and to generate assembled contigs with a good coverage of genome and genes. In addition, we observed that the assembly-based approach had a much lower recall rate and precision comparing to the alignment-based approach that would recover 99% of imputed SNVs. We observed similar results with experimental reads for NA24385, an individual whose germline variants were well characterized. Although there are additional values for SNVs detection, the assembly-based approach would have great risk of false discovery of novel SNVs. Further improvement of de novo assembly algorithms are needed in order to warrant a good completeness of genome with haplotype resolved and high fidelity of assembled sequences.
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