SARS-CoV-2 transmission analysis of two genome datasets

[Description of methods used for collection/generation of data] Worldwide surveys using the GISAID EpiCov database were conducted on 2022-01-16 and 2022-06-15, resulting in the collection of two SARS-CoV-2 genome datasets. Then, transcluster v2.0.0 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. Further pipeline documentation is available at https://github.com/PathoGenOmics-Lab/transcluster. [Methods for processing the data] Raw genome data from GISAID was processed using transcluster v2.0.0 (https://github.com/PathoGenOmics-Lab/transcluster). The input lists contain the sample identifiers that were selected after filtering by haplotype and sequence quality.