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gofasta: command-line utilities for genomic epidemiology research
1Institute of Ecology and Evolution, University of Edinburgh, Edinburgh EH9 3FL, UK.
Bioinformatics (Oxford, England)
|July 5, 2022
Summary
gofasta is a new software tool for analyzing pathogen genomic data, particularly useful for tracking outbreaks like SARS-CoV-2. It efficiently handles large datasets and identifies genetic variations for epidemiological studies.
Area of Science:
- Genomic epidemiology
- Bioinformatics
- Computational biology
Background:
- Genomic epidemiology relies on analyzing pathogen genomes to understand disease transmission.
- Processing large datasets of closely related viral genomes, such as SARS-CoV-2, presents computational challenges.
Purpose of the Study:
- To introduce gofasta, a command-line utility suite designed for genomic epidemiology.
- To provide efficient tools for handling and analyzing assembled short genomes.
Main Methods:
- gofasta offers functions to convert sequence alignment formats (SAM to FASTA).
- It annotates mutations within multiple sequence alignments.
- It enables extraction of sequence sets based on genetic distance for outbreak investigations.
Main Results:
- gofasta facilitates the processing of large numbers of closely related viral genomes.
- The software is particularly suited for SARS-CoV-2 genomic data.
- It supports analysis of other densely sampled pathogen genomic datasets.
Conclusions:
- gofasta provides essential utilities for genomic epidemiology workflows.
- The tool enhances the ability to investigate outbreaks using genomic data.
- Its open-source nature and availability promote widespread adoption.
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