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

This project contains data associated with our paper, Transposable elements are driving rapid adaptation of Enterococcus faecium (Grieshop & Behr et al., Nature, 2026) [doi link]. For a lay-overview of this study, check out the associated Research Briefing. Note: If you utilize any of the data or analyses found in this project, please cite our work. 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 our paper'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 our paper (i.e., figure source data for Fig. 2A and Extended Data Fig. 7). Other figure source data is included with the manuscript itself. 4. Deposited archive of codebase The gzipped tarball is-evolution-codebase-snapshot.tar.gz contains a snapshot (d0bb2b3, 2026-03-04) of the codebase and workflows underlying the analyses presented in our manuscript. The most up-to-date version can be found on GitHub at https://github.com/abehr/is-evolution.