Data: Guiding the design of SARS-CoV-2 genomic surveillance by estimating the resolution of outbreak detection

Contains data necessary to reproduce the quantitative results related to a SARS-CoV-2 outbreak in NSW, Australia in the associated paper.

icpmr_delta_gisaid.csv
Tabular data containing the GISAID accession numbers, dates of collection and submission for all sequences used in the NSW outbreak analysis. The epi set is available on GISAID as EPI_SET_220919ef. The wgs_cluster column contains identifiers of genomic clusters defined at ICPMR, NSW Health Pathology. A value of "Other" means that the sequence either did not belong to a cluster or was part of a cluster that contained fewer than 30 sequences in the study period, and sequences with this value should not be considered to form a single cluster.

icpmr_delta_gisaid.dists.tsv.gz
Compressed pairwise SNP distance matrix in the format output by snp-dists. The script that creates this file from sequence data is available in the linked code archive.