SARS-CoV-2 survey of reads data and transmission analysis of two datasets

Processed data, code, configuration files and main results of a survey of raw reads data and the transmission analysis of two datasets of SARS-CoV-2 records assigned to the BA.1 Omicron lineage carrying spike NTD deletion repairs. The survey brought out 1,541,892 matching records as of 10 December 2024, of which 464,859 records selected at random for further analysis. For each, FASTQ files were retrieved from via the ENA Portal API and processed to detect the specific genetic variants. For the transmission analysis, aligned genomes were placed on a mutation-annotated tree, and 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. The source code is included here, and is also available in GitHub (survey: https://github.com/PathoGenOmics-Lab/ena-spike-ntd-repdel-analysis; transmission estimation: https://github.com/PathoGenOmics-Lab/transcluster).