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

[Description of methods used for collection/generation of data] A worldwide survey using the GISAID EpiCov database was conducted on 2022-06-15, resulting in the collection of a SARS-CoV-2 genome dataset. Another worldwide survey using the ENA database was conducted on 2024-12-10. The second survey returned raw reads, and so the code and main processed files are made available here. The "output" folder contains the pipeline output files, including lineage assignment and repaired deletion identification results. Then, transcluster v2.1.0 was run on these datasets. For each dataset, input files containing lists of sample identifiers are contained in the "input" folder. The "output" folder contains the pipeline output files, consisting on a separate folder for each of the input lists, as well as a "summary" folder. Each "config/config.yaml" file describes the pipeline configuration of each run.