Fast and accurate mapping of long reads to complete genome assemblies with VerityMap

Andrey V Bzikadze; Alla Mikheenko; Pavel A Pevzner

doi:10.1101/gr.276871.122

Fast and accurate mapping of long reads to complete genome assemblies with VerityMap

Genome Res. 2022 Nov-Dec;32(11-12):2107-2118. doi: 10.1101/gr.276871.122. Epub 2022 Nov 15.

Authors

Andrey V Bzikadze^#¹, Alla Mikheenko^#², Pavel A Pevzner³

Affiliations

¹ Graduate Program in Bioinformatics and Systems Biology, University of California, San Diego, California 92093, USA.
² Center for Algorithmic Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia.
³ Department of Computer Science and Engineering, University of California, San Diego, California 92093, USA.

^# Contributed equally.

Abstract

Recent advancements in long-read sequencing have enabled the telomere-to-telomere (complete) assembly of a human genome and are now contributing to the haplotype-resolved complete assemblies of multiple human genomes. Because the accuracy of read mapping tools deteriorates in highly repetitive regions, there is a need to develop accurate, error-exposing (detecting potential assembly errors), and diploid-aware (distinguishing different haplotypes) tools for read mapping in complete assemblies. We describe the first accurate, error-exposing, and partially diploid-aware VerityMap tool for long-read mapping to complete assemblies.

Publication types

Research Support, U.S. Gov't, Non-P.H.S.
Research Support, Non-U.S. Gov't

MeSH terms

Diploidy
Genome, Human*
High-Throughput Nucleotide Sequencing*
Humans
Repetitive Sequences, Nucleic Acid
Sequence Analysis, DNA