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.

SUMMARY: The variant call format (VCF) is a popular standard for storing genetic variation data. As a result, a large collection of tools has been developed that perform diverse analyses using VCF files. However, some tasks common to statistical and population geneticists have not been created yet. To streamline these types of analyses, we created novel tools that analyze or annotate VCF files and organized these tools into a command-line based utility named VCF-kit. VCF-kit adds essential utilities to process and analyze VCF files, including primer generation for variant validation, dendrogram production, genotype imputation from sequence data in linkage studies, and additional tools. AVAILABILITY AND IMPLEMENTATION: https://github.com/AndersenLab/VCF-kit. CONTACT: [email protected].