gofasta

gofasta processes and analyzes genome alignments to support genomic epidemiology of short assembled genomes, including densely sampled pathogens such as SARS-CoV-2.

Key Features:

• Alignment conversion: Converts SAM-format pairwise alignments between assembled genomes into FASTA-format sequences.
• Mutation annotation: Annotates mutations within multiple sequence alignments to report variant positions and changes.
• Genetic distance extraction: Extracts sets of sequences based on genetic distance measures to identify closely related strains.

Scientific Applications:

• SARS-CoV-2 genomic surveillance: Processes large-scale SARS-CoV-2 datasets, including workflows handling millions of sequences.
• Outbreak investigation: Identifies closely related genomes and mutation patterns to inform transmission and cluster analyses.
• Integration in analysis pipelines: Serves as a component in genome-processing pipelines such as Pangolin and Civet for daily SARS-CoV-2 analyses.

Methodology:

Converting SAM-format pairwise alignments to FASTA, annotating mutations in multiple sequence alignments, extracting sequences by genetic distance, and scaling these operations for large datasets of closely related genomes.