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Pangenomic genotyping with the marker array.

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Bibliographic Details
Title: Pangenomic genotyping with the marker array.
Authors: Mun, Taher1 (AUTHOR), Vaddadi, Naga Sai Kavya1 (AUTHOR), Langmead, Ben1 (AUTHOR) langmea@cs.jhu.edu
Source: Algorithms for Molecular Biology. 5/5/2023, Vol. 18 Issue 1, p1-17. 17p.
Subject Terms: *OPEN source software, *GENETIC software, *SOFTWARE development tools
Abstract: We present a new method and software tool called rowbowt that applies a pangenome index to the problem of inferring genotypes from short-read sequencing data. The method uses a novel indexing structure called the marker array. Using the marker array, we can genotype variants with respect from large panels like the 1000 Genomes Project while reducing the reference bias that results when aligning to a single linear reference. rowbowt can infer accurate genotypes in less time and memory compared to existing graph-based methods. The method is implemented in the open source software tool rowbowt available at https://github.com/alshai/rowbowt. [ABSTRACT FROM AUTHOR]
Database: Academic Search Index
Description
Abstract:We present a new method and software tool called rowbowt that applies a pangenome index to the problem of inferring genotypes from short-read sequencing data. The method uses a novel indexing structure called the marker array. Using the marker array, we can genotype variants with respect from large panels like the 1000 Genomes Project while reducing the reference bias that results when aligning to a single linear reference. rowbowt can infer accurate genotypes in less time and memory compared to existing graph-based methods. The method is implemented in the open source software tool rowbowt available at https://github.com/alshai/rowbowt. [ABSTRACT FROM AUTHOR]
ISSN:17487188
DOI:10.1186/s13015-023-00225-3