Escherichia coli lineage deconvolution indexes for Themisto, mSWEEP/mGEMS, and demix_check This dataset contains the indexes used in a study conducted in Punjab, Pakistan that investigated E. coli colonisation diversity in healthy carriage with the use of CLED enrichment plates. The following files are included in the download: Themisto v3 pseudoalignment index. PopPUNK database. Demix_check index. Raw assembly data. About Version history v0.1.0 (current version) Added brief description with a few missing parts. Distribution These files are made available under a CC-BY 4.0 license. If you use these assemblies in your study please cite the source as appropriate (study will be added in a later version). Methods briefly Data Assembly data included originates from the following studies: Horesh G, et al., A comprehensive and high-quality collection of Escherichia coli genomes and their genes. Microbial Genomics 2021. doi: 10.1099/mgen.0.000499 Gladstone R, et al., Emergence and dissemination of antimicrobial resistance in Escherichia coli causing bloodstream infections in Norway in 2002–17: a nationwide, longitudinal, microbial population genomic study. The Lancet Microbe 2021. doi: 10.1016/S2666-5247(21)00031-8 Shao Y, et al., Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth. Nature 2019. 10.1038/s41586-019-1560-1 Snaith AE, et al. The highly diverse plasmid population found in Escherichia coli colonizing travellers to Laos and its role in antimicrobial resistance gene carriage. Microbial Genomics 2023. doi: 10.1099/mgen.0.001000 Habib A, et al. Dissemination of carbapenemase-producing Enterobacterales in the community of Rawalpindi, Pakistan. PLOS ONE 2022. doi: 10.1371/journal.pone.0270707 Runcharoen C, et al. Whole genome sequencing of ESBL-producing Escherichia coli isolated from patients, farm waste and canals in Thailand. Genome Medicine 2017. doi: 10.1186/s13073-017-0471-8 Musicha P, et al. Trends in antimicrobial resistance in bloodstream infection isolates at a large urban hospital in Malawi (1998–2016): a surveillance study. The Lancet Infectious Diseases 2017. doi: 10.1016/S1473-3099(17)30394-8 Themisto index construction Assemblies were indexed with Themisto v3.0.0-rc using k-mer size 31 and the `--file-colors` option. PopPUNK clustering We followed the approach described in Mäklin et al. 2022 using PopPUNK v2.5.0. Demix check indexing The index was generated using the `setup_reference.sh` script from tmaklin/coreutils_demix_check. Contact Tommi Mäklin .