{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,16]],"date-time":"2026-04-16T00:17:35Z","timestamp":1776298655265,"version":"3.50.1"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"16","license":[{"start":{"date-parts":[[2022,7,5]],"date-time":"2022-07-05T00:00:00Z","timestamp":1656979200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Medical Research Council (MRC) part of UK Research & Innovation"},{"DOI":"10.13039\/501100000272","name":"National Institute of Health Research","doi-asserted-by":"crossref","award":["MC_PC_19027"],"award-info":[{"award-number":["MC_PC_19027"]}],"id":[{"id":"10.13039\/501100000272","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Genome Research Limited, operating as the Wellcome Sanger Institute"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,8,10]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Summary<\/jats:title><jats:p>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.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>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\u2019s package management system. Source code and further documentation, including walkthroughs for common use cases, are available on the GitHub repository.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac424","type":"journal-article","created":{"date-parts":[[2022,7,5]],"date-time":"2022-07-05T13:47:10Z","timestamp":1657028830000},"page":"4033-4035","source":"Crossref","is-referenced-by-count":28,"title":["gofasta: command-line utilities for genomic epidemiology research"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9981-0649","authenticated-orcid":false,"given":"Ben","family":"Jackson","sequence":"first","affiliation":[{"name":"Institute of Ecology and Evolution, University of Edinburgh , Edinburgh EH9 3FL, UK"}]}],"member":"286","published-online":{"date-parts":[[2022,7,5]]},"reference":[{"key":"2023041408473821700_","doi-asserted-by":"crossref","first-page":"3773","DOI":"10.21105\/joss.03773","article-title":"Nextclade: clade assignment, mutation calling and quality control for viral genomes","volume":"6","author":"Aksamentov","year":"2021","journal-title":"J. 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