Genofunc: Genome annotation and identification of genome features for automated pipelining analysis of virus whole genome sequences

Research output: Contribution to journalArticlepeer-review

Abstract / Description of output

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
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
Genofunc is implemented fully in Python and licensed under the MIT license. Source code and documentation is available at: https://github.com/xiaoyu518/genofunc.
Original languageEnglish
Article number218
Number of pages6
JournalBMC Bioinformatics
Volume24
DOIs
Publication statusPublished - 30 May 2023

Keywords / Materials (for Non-textual outputs)

  • genome annotation
  • bioinformatics pipeline
  • phylogenetics
  • virus

Fingerprint

Dive into the research topics of 'Genofunc: Genome annotation and identification of genome features for automated pipelining analysis of virus whole genome sequences'. Together they form a unique fingerprint.

Cite this