Datasets for 'Mandrake: visualising microbial population structure by embedding millions of genomes into a low-dimensional representation'

Datasets for the paper 'Mandrake: visualising microbial population structure by embedding millions of genomes into a low-dimensional representation'

Files:

616k* - Files for the analysis of 661k bacterial genomes from the SRA (note typo 616-661k). Includes mandrake output and input files (.npz)

gps_acc - Files for the analysis of 20k S. pneumoniae accessory genomes from the GPS project. Original accessory matrix is gps_gene_presence_absence.Rtab

sc2million_v1* - Files for the analysis of ~1M SARS-CoV-2 genomes. sc2million_v3.npz are the input distances.

sce.qdrep - Nvidia systems profile of code at that commit hash

sce.ncu-rep - Nvidia kernel profile of code at that commit hash