Publication Date
10-5-2023
Journal
Genome Biology
DOI
10.1186/s13059-023-03061-1
PMID
37798733
PMCID
PMC10552390
PubMedCentral® Posted Date
10-5-2023
PubMedCentral® Full Text Version
Post-print
Published Open-Access
yes
Keywords
Benchmarking, Genomics, Computational Biology, Genome, High-Throughput Nucleotide Sequencing, Genetic variation, SNPs, Indels, Structural variant, Benchmark datasets, Medical genes, Sequencing technology
Abstract
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.
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Biological Phenomena, Cell Phenomena, and Immunity Commons, Biomedical Informatics Commons, Genetics and Genomics Commons, Medical Genetics Commons, Medical Molecular Biology Commons, Medical Specialties Commons