Journal
BIOINFORMATICS
Volume 38, Issue 16, Pages 4033-4035Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btac424
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Funding
- Medical Research Council (MRC) part of UK Research & Innovation (UKRI)
- National Institute of Health Research (NIHR) [MC_PC_19027]
- Genome Research Limited
- Wellcome Sanger Institute
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gofasta is a set of command-line utilities designed for handling short assembled genomes in the context of genomic epidemiology. It was specifically developed for processing closely related SARS-CoV-2 viral genomes and can also be applied to other densely sampled pathogen genomic datasets. It offers functions to convert sam-format pairwise alignments to fasta format, annotate mutations in multiple sequence alignments, and extract sets of sequences based on genetic distance measures for outbreak investigations.
A 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.
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