2026-10-06T19:24:13Z https://api.figshare.com/v2/oai

oai:figshare.com:article/33965176 2026-09-22T13:46:10Z category_24310 category_24208 category_24361 item_type_3 month_year_09_2026

Mycobacteriaceae database for mashID - 2026-09-22 update Marc-Olivier Duceppe (11048067) Genomics Bioinformatics and computational biology not elsewhere classified Microbial genetics mashID Mash MinHash Mycobacteriaceae Mycobacterium Mycobacterium tuberculosis complex Mycobacterium bovis nontuberculous mycobacteria species identification bacterial identification whole genome sequencing sketch database reference database <p dir="ltr">Mash sketch database of the family Mycobacteriaceae (NCBI taxon 1762) for species identification with mashID (https://github.com/duceppemo/mashID).</p><p dir="ltr">Contents</p><p dir="ltr">- mycobacteriaceae_2026-09-22.msh: Mash 2.3 sketches, k-mer size 21, sketch size 10000, 3534 reference genomes (284 MB). MD5: cc73df8b8b5f7257849c6039430f2a43</p><p dir="ltr">- mycobacteriaceae_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 16,189 GenBank assemblies of taxon 1762 available on 2026-09-22 were downloaded with NCBI Datasets (atypical assemblies excluded), 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 3534 representatives (Mycobacterium tuberculosis: 211 of 8722). References shorter than 100 kb were excluded. Organism names and TaxIDs come from the NCBI assembly report; strain designations were removed from names. The build is reproducible with scripts/build_mycobacteriaceae_db.sh in the mashID repository.</p><p dir="ltr">Usage</p><p dir="ltr">mashID -i reads/ -o results -d mycobacteriaceae_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 2025-02-20 release: ten times larger sketches (finer identities), NCBI TaxIDs for every reference, no partial records, and the Mycobacterium / Mycolicibacterium / Mycobacteroides synonyms are resolved through NCBI names.</p><p dir="ltr">Note: Mash separates species, not members of the Mycobacterium tuberculosis complex; use SNP-based methods for variants and lineages.</p> 2026-09-22T13:46:10Z Dataset Dataset 10.6084/m9.figshare.33965176.v1 https://figshare.com/articles/dataset/Mycobacteriaceae_database_for_mashID_-_2026-09-22_update/33965176 CC BY 4.0