G2GSnake: a Snakemake workflow for host-pathogen genomic association studies.
Journal
Bioinformatics advances
ISSN: 2635-0041
Titre abrégé: Bioinform Adv
Pays: England
ID NLM: 9918282081306676
Informations de publication
Date de publication:
2023
2023
Historique:
received:
26
04
2023
revised:
27
09
2023
accepted:
03
10
2023
medline:
16
10
2023
pubmed:
16
10
2023
entrez:
16
10
2023
Statut:
epublish
Résumé
Joint analyses of paired host and pathogen genome sequences have the potential to enhance our understanding of host-pathogen interactions. A systematic approach to conduct such a joint analysis is through a "genome-to-genome" (G2G) association study, which involves testing for associations between all host and pathogen genetic variants. Significant associations reveal host genetic factors that might drive pathogen variation, highlighting biological mechanisms likely to be involved in host control and pathogen escape. Here, we present a Snakemake workflow that allows researchers to conduct G2G studies in a reproducible and scalable manner. In addition, we have developed an intuitive R Shiny application that generates custom summaries of the results, enabling users to derive relevant insights. G2GSnake is freely available at: https://github.com/zmx21/G2GSnake under the MIT license.
Identifiants
pubmed: 37840906
doi: 10.1093/bioadv/vbad142
pii: vbad142
pmc: PMC10576169
doi:
Types de publication
Journal Article
Langues
eng
Pagination
vbad142Informations de copyright
© The Author(s) 2023. Published by Oxford University Press.
Déclaration de conflit d'intérêts
O.N. is now an employee of SUN bioscience SA.
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