SARS-CoV-2 transmission analysis of two genome datasets

Processed data, code, configuration files and results of the transmission analysis of two datasets of SARS-CoV-2 genomes. The first dataset contains samples bearing combinations of Alpha and Delta-defining NTD mutations. The second dataset contains samples assigned to the Alpha variant and the BA.1 Omicron lineage with NTD deletion repairs. The GISAID EPI_SETs are available at https://dx.doi.org/10.55876/gis8.230802fh and https://dx.doi.org/10.55876/gis8.230801ex, respectively. The sequence records from each list of target samples were extracted from a FASTA file containing an aligned sequence dataset, and placed on a reference phylogeny. Then, transmission clusters were detected using a breadth-first search approach. Additionally, a fitness metric was estimated for each cluster. Finally, a series of figures (including sample timelines, comparisons of estimated fitness and missing data) were generated. The pipeline used for this analysis, transcluster v2.0.0, is a Snakemake workflow released as free software under the GNU GPLv3 license. Its source code is included here, and is also available in GitHub (https://github.com/PathoGenOmics-Lab/transcluster).