An SGSGeneloss-Based Method for Constructing a Gene Presence-Absence Table Using Mosdepth.

Autor:	Tay Fernandez CG; Applied Bioinformatics Group, School of Biological Sciences, The University of Western Australia, Perth, WA, Australia., Marsh JI; Applied Bioinformatics Group, School of Biological Sciences, The University of Western Australia, Perth, WA, Australia., Nestor BJ; Applied Bioinformatics Group, School of Biological Sciences, The University of Western Australia, Perth, WA, Australia., Gill M; Applied Bioinformatics Group, School of Biological Sciences, The University of Western Australia, Perth, WA, Australia., Golicz AA; Department of Plant Breeding, Justus Liebig University Gießen, Gießen, Germany., Bayer PE; Applied Bioinformatics Group, School of Biological Sciences, The University of Western Australia, Perth, WA, Australia., Edwards D; Applied Bioinformatics Group, School of Biological Sciences, The University of Western Australia, Perth, WA, Australia. dave.edwards@uwa.edu.au.
Jazyk:	angličtina
Zdroj:	Methods in molecular biology (Clifton, N.J.) [Methods Mol Biol] 2022; Vol. 2512, pp. 73-80.
DOI:	10.1007/978-1-0716-2429-6_5
Abstrakt:	Presence-absence variants (PAV) are genomic regions present in some individuals of a species, but not others. PAVs have been shown to contribute to genomic diversity, especially in bacteria and plants. These structural variations have been linked to traits and can be used to track a species' evolutionary history. PAVs are usually called by aligning short read sequence data from one or more individuals to a reference genome or pangenome assembly, and then comparing coverage. Regions where reads do not align define absence in that individual, and the regions are classified as PAVs. The method below details how to align sequence reads to a reference and how to use the sequencing-coverage calculator Mosdepth to identify PAVs and construct a PAV table for use in downstream comparative genome analysis. (© 2022. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)
Databáze:	MEDLINE
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