An SGSGeneloss-Based Method for Constructing a Gene Presence-Absence Table Using Mosdepth.
Methods Mol Biol
; 2512: 73-80, 2022.
Article
em En
| MEDLINE
| ID: mdl-35818000
ABSTRACT
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.
Palavras-chave
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Genoma
/
Genômica
Tipo de estudo:
Prognostic_studies
Limite:
Humans
Idioma:
En
Revista:
Methods Mol Biol
Assunto da revista:
BIOLOGIA MOLECULAR
Ano de publicação:
2022
Tipo de documento:
Article
País de afiliação:
Austrália