2026-10-08T20:32:00Z https://api.figshare.com/v2/oai

oai:figshare.com:article/33968620 2026-09-22T19:07:53Z category_24310 category_24361 category_24208 item_type_3 month_year_09_2026

Listeria database for mashID - 2026-09-22 update Marc-Olivier Duceppe (11048067) Genomics Microbial genetics Bioinformatics and computational biology not elsewhere classified mashID Mash MinHash Listeria Listeria monocytogenes Listeria ivanovii species identification bacterial identification whole genome sequencing sketch database reference database <p dir="ltr">Mash sketch database of the genus Listeria (NCBI taxon 1637) for species identification with mashID (https://github.com/duceppemo/mashID).</p><p dir="ltr">Contents</p><p dir="ltr">- listeria_2026-09-22.msh: Mash 2.3 sketches, k-mer size 21, sketch size 10000, 1441 reference genomes covering 42 Listeria species and subspecies (116 MB). MD5: 4d0f8f53d71dbcea526508f1b246ab2f</p><p dir="ltr">- listeria_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 7453 RefSeq assemblies of taxon 1637 available on 2026-09-22 were downloaded with NCBI Datasets (atypical assemblies excluded; RefSeq rather than GenBank, whose 79,000 mostly L. monocytogenes assemblies are largely redundant), binned by species using the organism name of the NCBI assembly report, and dereplicated within each species with Assembly-dereplicator 0.3.2 at a Mash distance of 0.001 (99.9% identity), keeping 1441 representatives (L. monocytogenes: 892 of 6,800). Organism names and TaxIDs come from the NCBI assembly report. The build is reproducible with scripts/build_mycobacteriaceae_db.sh in the mashID repository (ASSEMBLY_SOURCE=RefSeq, taxon 1637).</p><p dir="ltr">Usage</p><p dir="ltr">mashID -i reads/ -o results -d listeria_2026-09-22.msh</p><p dir="ltr">Keep the .metadata.tsv file next to the .msh file.</p><p dir="ltr">Compared with the 2025-02-18 release: NCBI TaxIDs for every reference, names from NCBI rather than parsed headers, sketch size 10000.</p> 2026-09-22T19:07:53Z Dataset Dataset 10.6084/m9.figshare.33968620.v1 https://figshare.com/articles/dataset/Listeria_database_for_mashID_-_2026-09-22_update/33968620 CC BY 4.0