gofasta: command-line utilities for genomic epidemiology research.
Bioinformatics
; 38(16): 4033-4035, 2022 Aug 10.
Article
in English
| MEDLINE | ID: covidwho-1922198
ABSTRACT
SUMMARY:
gofasta comprises a set of command-line utilities for handling alignments of short assembled genomes in a genomic epidemiology context. It was developed for processing large numbers of closely related SARS-CoV-2 viral genomes and should be useful with other densely sampled pathogen genomic datasets. It provides functions to convert sam-format pairwise alignments between assembled genomes to fasta format; to annotate mutations in multiple sequence alignments, and to extract sets of sequences by genetic distance measures for use in outbreak investigations. AVAILABILITY AND IMPLEMENTATION gofasta is an open-source project distributed under the MIT license. Binaries are available at https//github.com/virus-evolution/gofasta, from Bioconda, and through the Go programming language's package management system. Source code and further documentation, including walkthroughs for common use cases, are available on the GitHub repository.
Full text:
Available
Collection:
International databases
Database:
MEDLINE
Main subject:
SARS-CoV-2
/
COVID-19
Type of study:
Observational study
Limits:
Humans
Language:
English
Journal:
Bioinformatics
Journal subject:
Medical Informatics
Year:
2022
Document Type:
Article
Affiliation country:
Bioinformatics
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