2026-10-06T11:02:25Z https://api.figshare.com/v2/oai

oai:figshare.com:article/33969760 2026-09-23T03:25:56Z category_24310 category_24361 category_24208 item_type_3 month_year_09_2026

Escherichia and Shigella database for mashID - 2026-09-22 Marc-Olivier Duceppe (11048067) Genomics Microbial genetics Bioinformatics and computational biology not elsewhere classified mashID Mash MinHash Escherichia coli Escherichia Shigella species identification bacterial identification whole genome sequencing sketch database reference database <p dir="ltr">Mash sketch database of the genera Escherichia (NCBI taxon 561) and Shigella (taxon 620) for species-level identification with mashID (https://github.com/duceppemo/mashID).</p><p dir="ltr">Contents</p><p dir="ltr">- escherichia_shigella_2026-09-22.msh: Mash 2.3 sketches, k-mer size 21, sketch size 10000, 4503 reference genomes: Escherichia coli (3316), E. albertii, E. fergusonii, E. marmotae, E. ruysiae, E. whittamii, Shigella sonnei, S. flexneri, S. boydii and S. dysenteriae (362 MB). MD5: 0a8a7b18f9dec77ce8578116d115d18b</p><p dir="ltr">- escherichia_shigella_2026-09-22.metadata.tsv: one line per reference with accession, organism name, NCBI TaxID, genome length, sketch hash count, source file and original fasta header. mashID reads it automatically when it sits next to the .msh file.</p><p dir="ltr">Construction</p><p dir="ltr">All 53,845 Escherichia and 3,301 Shigella RefSeq assemblies available on 2026-09-22 were downloaded with NCBI Datasets (atypical assemblies excluded), binned by species from the NCBI assembly report, each bin capped at 5000 assemblies keeping complete genomes first (for E. coli this retains the 5595 complete genomes, none of the draft ones), and dereplicated within each bin with Assembly-dereplicator 0.3.2 at a Mash distance of 0.001 (99.9% identity). Assemblies named only "Escherichia sp." or "Shigella sp." were excluded. Organism names and TaxIDs come from the NCBI assembly report. Reproducible with scripts/build_taxon_db.sh in the mashID repository (ASSEMBLY_SOURCE=RefSeq, MAX_BIN=5000, EXCLUDE_SP=1, taxa 561,620).</p><p dir="ltr">Validation</p><p dir="ltr">On 251 RefSeq genomes not included in the database (up to 30 per species), mashID reported the NCBI species for 96.4%. All Escherichia species other than E. coli were 100% concordant; the discordant cases were Shigella boydii, S. dysenteriae and S. flexneri genomes matched to another Shigella species at over 99.9% identity, and two E. coli genomes matched to S. sonnei.</p><p dir="ltr">Scope</p><p dir="ltr">Shigella species are lineages of E. coli named by serotype, and S. boydii, S. dysenteriae and S. flexneri share lineages, so mashID separates E. coli from the clonal S. sonnei and S. flexneri groups well but cannot reliably distinguish the other Shigella species from each other or enteroinvasive E. coli from Shigella. Use ShigaTyper or ShigEiFinder for that, and ECTyper or SerotypeFinder for E. coli serotypes.</p> 2026-09-23T03:25:56Z Dataset Dataset 10.6084/m9.figshare.33969760.v1 https://figshare.com/articles/dataset/Escherichia_and_Shigella_database_for_mashID_-_2026-09-22/33969760 CC BY 4.0