Genofunc: genome annotation and identification of genome features for automated pipelining analysis of virus whole genome sequences.
Bioinformatics pipeline
Genome annotation
Phylogenetics
Virus
Journal
BMC bioinformatics
ISSN: 1471-2105
Titre abrégé: BMC Bioinformatics
Pays: England
ID NLM: 100965194
Informations de publication
Date de publication:
30 May 2023
30 May 2023
Historique:
received:
25
01
2023
accepted:
25
05
2023
medline:
1
6
2023
pubmed:
31
5
2023
entrez:
30
5
2023
Statut:
epublish
Résumé
Viral genomics and epidemiology have been increasingly important tools for analysing the spread of key pathogens affecting daily lives of individuals worldwide. With the rapidly expanding scale of pathogen genome sequencing efforts for epidemics and outbreaks efficient workflows in extracting genomic information are becoming increasingly important for answering key research questions. Here we present Genofunc, a toolkit offering a range of command line orientated functions for processing of raw virus genome sequences into aligned and annotated data ready for analysis. The tool contains functions such as genome annotation, feature extraction etc. for processing of large genomic datasets both manual or as part of pipeline such as Snakemake or Nextflow ready for down-stream phylogenetic analysis. Originally designed for a large-scale HIV sequencing project, Genofunc has been benchmarked against annotated sequence gene coordinates from the Los Alamos HIV database as validation with downstream phylogenetic analysis result comparable to past literature as case study. Genofunc is implemented fully in Python and licensed under the MIT license. Source code and documentation is available at: https://github.com/xiaoyu518/genofunc .
Sections du résumé
BACKGROUND
BACKGROUND
Viral genomics and epidemiology have been increasingly important tools for analysing the spread of key pathogens affecting daily lives of individuals worldwide. With the rapidly expanding scale of pathogen genome sequencing efforts for epidemics and outbreaks efficient workflows in extracting genomic information are becoming increasingly important for answering key research questions.
RESULTS
RESULTS
Here we present Genofunc, a toolkit offering a range of command line orientated functions for processing of raw virus genome sequences into aligned and annotated data ready for analysis. The tool contains functions such as genome annotation, feature extraction etc. for processing of large genomic datasets both manual or as part of pipeline such as Snakemake or Nextflow ready for down-stream phylogenetic analysis. Originally designed for a large-scale HIV sequencing project, Genofunc has been benchmarked against annotated sequence gene coordinates from the Los Alamos HIV database as validation with downstream phylogenetic analysis result comparable to past literature as case study.
CONCLUSION
CONCLUSIONS
Genofunc is implemented fully in Python and licensed under the MIT license. Source code and documentation is available at: https://github.com/xiaoyu518/genofunc .
Identifiants
pubmed: 37254048
doi: 10.1186/s12859-023-05356-3
pii: 10.1186/s12859-023-05356-3
pmc: PMC10227794
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
218Subventions
Organisme : Bill and Melinda Gates Foundation
ID : OPP1175094
Informations de copyright
© 2023. The Author(s).
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