Data for E. faecium ISL3 project: long-read Enterococcus genome resource + preprocessed data for manuscript analyses

# NOTE: This project and associated manuscript are WIP under review; publication information will be updated shortly. # Please contact the authors for more information. 1. Resource: long-read clinical Enterococcus genome assemblies The gzipped tarball ente_isolate_assemblies.tar.gz contains 282 new long-read genome assemblies from Enterococcus clinical isolates. Bloodstream infection isolates were collected between 2020-2024 at Stanford Hospitals. Isolates were sequenced (Oxford Nanopore, R10.4.1 chemistry) and assembled (Flye 2.9.1) in 2024. Included genomes: 107 E. faecium, 167 E. faecalis, 8 other enterococci. See the associated manuscript's Methods section for more detail. 2. Preprocessed source data for manuscript analyses The package analyses_preprocessed_source_data.zip contains preprocessed source data files that can be used to reproduce analyses and figures from the associated manuscript. More instructions can be found on our GitHub repository. 3. Phylogenetic trees The package trees_newick_source_files.zip contains newick files to produce the original trees from the associated manuscript (i.e., figure source data for Fig. 2A and Extended Data Fig. 7). Other figure source data is included with the manuscript itself.