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gofasta: command-line utilities for genomic epidemiology research.
Jackson, Ben.
  • Jackson B; Institute of Ecology and Evolution, University of Edinburgh, Edinburgh EH9 3FL, UK.
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.
Subject(s)

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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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