2026-10-06T16:52:24Z https://api.figshare.com/v2/oai

oai:figshare.com:article/33968917 2026-09-22T21:32:43Z category_24310 category_24361 category_24208 item_type_3 month_year_09_2026

Salmonella database for mashID - 2026-09-22 Marc-Olivier Duceppe (11048067) Genomics Microbial genetics Bioinformatics and computational biology not elsewhere classified mashID Mash MinHash Salmonella Salmonella enterica Salmonella bongori species identification subspecies bacterial identification whole genome sequencing sketch database reference database <p dir="ltr">Mash sketch database of the genus Salmonella (NCBI taxon 590) for species- and subspecies-level identification with mashID (https://github.com/duceppemo/mashID).</p><p dir="ltr">Contents</p><p dir="ltr">- salmonella_2026-09-22.msh: Mash 2.3 sketches, k-mer size 21, sketch size 10000, 1442 reference genomes covering Salmonella bongori and all six subspecies of Salmonella enterica (116 MB). MD5: 96fa827bad8e68a92713ead5019a3783</p><p dir="ltr">- salmonella_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 21,133 RefSeq assemblies of taxon 590 available on 2026-09-22 were downloaded with NCBI Datasets (atypical assemblies excluded), binned by subspecies using the organism name of the NCBI assembly report, capped at 3000 assemblies per bin keeping complete genomes first, and dereplicated within each bin with Assembly-dereplicator 0.3.2 at a Mash distance of 0.001 (99.9% identity). Assemblies named only "Salmonella sp." were excluded. Organism names and TaxIDs come from the NCBI assembly report. Reproducible with scripts/build_mycobacteriaceae_db.sh in the mashID repository (ASSEMBLY_SOURCE=RefSeq, BIN_RANK=subspecies, MAX_BIN=3000, taxon 590).</p><p dir="ltr">Usage</p><p dir="ltr">mashID -i reads/ -o results -d salmonella_2026-09-22.msh</p><p dir="ltr">Keep the .metadata.tsv file next to the .msh file.</p><p dir="ltr">Scope</p><p dir="ltr">This database identifies Salmonella to species and subspecies. Reference names include the serovar recorded by NCBI, so the reported name is that of the nearest reference genome; it is not a serotype determination.</p><p dir="ltr">Use antigen-based tools such as SeqSero2 or SISTR for serotyping.</p> 2026-09-22T21:32:43Z Dataset Dataset 10.6084/m9.figshare.33968917.v1 https://figshare.com/articles/dataset/Salmonella_database_for_mashID_-_2026-09-22/33968917 CC BY 4.0