Escherichia and Shigella database for mashID - 2026-09-22

<p dir="ltr">Mash sketch database of the genera Escherichia (NCBI taxon 561) and Shigella (taxon 620) for species-level identification with mashID (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).