Genomic variant benchmark: if you cannot measure it, you cannot improve it.

TitleGenomic variant benchmark: if you cannot measure it, you cannot improve it.
Publication TypeJournal Article
Year of Publication2023
AuthorsMajidian, S, Agustinho, DPaiva, Chin, C-S, Sedlazeck, FJ, Mahmoud, M
JournalGenome Biol
Date Published2023 Oct 05
KeywordsBenchmarking, Computational Biology, Genome, Genomics, High-Throughput Nucleotide Sequencing

Genomic benchmark datasets are essential to driving the field of genomics and bioinformatics. They provide a snapshot of the performances of sequencing technologies and analytical methods and highlight future challenges. However, they depend on sequencing technology, reference genome, and available benchmarking methods. Thus, creating a genomic benchmark dataset is laborious and highly challenging, often involving multiple sequencing technologies, different variant calling tools, and laborious manual curation. In this review, we discuss the available benchmark datasets and their utility. Additionally, we focus on the most recent benchmark of genes with medical relevance and challenging genomic complexity.

Alternate JournalGenome Biol
PubMed ID37798733
PubMed Central IDPMC10552390
Grant ListU01 HG011758 / HG / NHGRI NIH HHS / United States
U19 AI144297 / AI / NIAID NIH HHS / United States

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