ArticleBioinformatics (Oxford, England)2022
gofasta: command-line utilities for genomic epidemiology research.
Article in Bioinformatics (Oxford, England), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- The detection of three independent benzimidazole resistance mutations in a single Ancylostoma caninum population from a Golden Retriever breeding kennel in Sao Paulo, Brazil.International journal for parasitology. Drugs and drug resistance · 2026Article
- Disentangling SARS-CoV-2 Sustained Viremia Cases: Evolution, Persistence and Reinfection.Viruses · 2026Article
- Antibody escape drives emergence of diverse spike haplotypes resembling variants of concern in persistent SARS-CoV-2 infections.Cell reports. Medicine · 2026Article
- Human outbreak detection and best practice MPXV analysis and interpretation with squirrel.Virus evolution · 2026Article
- Long-term serial passaging of SARS-CoV-2 reveals signatures of convergent evolution.Journal of virology · 2025Article
- Comparison of pharyngeal and invasive isolates ofMicrobiology spectrum · 2025Article
- Pilot study: a descriptive-retrospective analysis of SARS-CoV-2 variants distribution and phylogenesis in the Phlegraean area.Frontiers in molecular biosciences · 2025Article
- Genomic analysis of the SARS-CoV-2 variants circulated in the Philippines, 2020-2024.Dialogues in health · 2024Article
- Human movement and environmental barriers shape the emergence of dengue.Nature communications · 2024Article
- Distinct evolution of SARS-CoV-2 Omicron XBB and BA.2.86/JN.1 lineages combining increased fitness and antibody evasion.Nature communications · 2024Article
- Distinct evolution of SARS-CoV-2 Omicron XBB and BA.2.86/JN.1 lineages combining increased fitness and antibody evasion.bioRxiv : the preprint server for biology · 2024Article
- A phylogenetics and variant calling pipeline to support SARS-CoV-2 genomic epidemiology in the UK.Virus evolution · 2024Article
- Utilizing river and wastewater as a SARS-CoV-2 surveillance tool in settings with limited formal sewage systems.Nature communications · 2023Article
- APOBEC3F Is a Mutational Driver of the Human Monkeypox Virus Identified in the 2022 Outbreak.The Journal of infectious diseases · 2023Article
- SCORPIO: a utility for defining and classifying mutation constellations of virus genomes.Bioinformatics (Oxford, England) · 2023Article
- Persistence of a Frameshifting Deletion in SARS-CoV-2 ORF7a for the Duration of a Major Outbreak.Viruses · 2023Article
- Genomics-informed outbreak investigations of SARS-CoV-2 using civet.PLOS global public health · 2022Article
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Abstract
summarygofasta 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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.