Fast and accurate mapping of long reads to complete genome assemblies with VerityMap
- 1Graduate Program in Bioinformatics and Systems Biology, University of California, San Diego, California 92093, USA;
- 2Center for Algorithmic Biotechnology, Saint Petersburg State University, Saint Petersburg, 199034, Russia;
- 3Department of Computer Science and Engineering, University of California, San Diego, California 92093, USA
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↵4 These authors contributed equally to this work.
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.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at https://www.genome.org/cgi/doi/10.1101/gr.276871.122.
- Received April 26, 2022.
- Accepted November 9, 2022.
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