PopPIPE subcluster results (S. pnuemoniae)

Results of running the PopPIPE pipeline (https://github.com/bacpop/PopPIPE) on the SPARC Streptococcus pneumoniae dataset (https://www.nature.com/articles/sdata201558).
sparc_tree.nwk. Originally published tree.full_tree.nwk. Output PopPIPE tree.all_clusters.txt. Subclusters from PopPIPE.microreact.json. Visualisation result, can be loaded into Microreact.mandrake_embedding.dot. Accessory clustering result (also included in microreact.json).sparc_subclusters.tar.bz2. Most output files from running all analysis steps. Some temporary files (.skf, map_variants.aln, transphylo_results.rds, gubbins.branch_base_reconstruction.embl) are excluded due to their size.transmission_metadata_renamed.csv. Can be used to run the transmission pipeline