Accurate human genome analysis with element avidity sequencing

• Published in: BMC bioinformatics Vol. 26; no. 1; pp. 194 - 12
• Main Authors: Carroll, Andrew, Kolesnikov, Alexey, Cook, Daniel E., Brambrink, Lucas, Wiseman, Kelly N., Billings, Sophie M., Kruglyak, Semyon, Lajoie, Bryan R., Zhao, Junhua, Levy, Shawn E., McLean, Cory Y., Shafin, Kishwar, Nattestad, Maria, Chang, Pi-Chuan
• Format: Journal Article
• Language: English
• Published: London BioMed Central 25.07.2025; BioMed Central Ltd; BMC
• Subjects: Accuracy; Algorithms; Avidity; Bioinformatics; Biomedical and Life Sciences; Candidates; Computational Biology/Bioinformatics; Computer Appl. in Life Sciences; DNA sequencing; Gene mapping; Gene sequencing; Genetic research; Genome, Human; Genomes; Genomic analysis; Genomics; Genomics - methods; High-Throughput Nucleotide Sequencing - methods; Human genetics; Humans; Innovations; Life Sciences; Methods; Microarrays; Nucleotide sequencing; Sequence Analysis, DNA - methods; Sequencing; Variant calling; WGS; Whole genome sequencing; Whole Genome Sequencing - methods; Y chromosomes; United States; WGS; Sequencing; Bioinformatics; Genomics; Variant calling
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-025-06191-4

Background New sequencing technologies provide options for the scientific community to design studies and build clinical workflows. These options expand user choice, and can enable more accurate, scalable, or affordable workflows depending on the fit between scientist needs and platform capability. However, it is essential to understand the performance of these new technologies for different tasks, especially for capabilities that were not possible or tractable in prior technologies. We investigate the new sequencing technology avidity from Element Biosciences. to help the scientific community understand the performance of the options to generate sequencing data. Results We show that Element whole genome sequencing achieves higher mapping and variant calling accuracy compared to Illumina sequencing at the same coverage, with larger differences at lower coverages (20–30x). We quantify base error rates of Element reads, finding lower error rates, especially in homopolymer and tandem repeat regions. We use Element’s ability to generate paired end sequencing with longer insert sizes than typical short–read sequencing. We show that longer insert sizes result in even higher accuracy, with long insert Element sequencing giving more accurate genome analyses at all coverages. Conclusions New options for sequencing technologies can analyze genomes comparably or better than prior standard methods.