gofasta: command-line utilities for genomic epidemiology research

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.

Automated summary

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.