2026-10-06T17:03:29Z https://api.figshare.com/v2/oai

oai:figshare.com:article/33968806 2026-09-22T20:31:31Z category_24310 category_24208 category_24361 item_type_3 month_year_09_2026

proGenomes 4 representative genomes database for mashID - 2026-09-22 Marc-Olivier Duceppe (11048067) Genomics Bioinformatics and computational biology not elsewhere classified Microbial genetics mashID Mash MinHash proGenomes bacteria archaea species identification bacterial identification whole genome sequencing sketch database reference database taxonomy <p dir="ltr">Mash sketch database of the proGenomes 4 representative genomes (https://progenomes.embl.de) for species-level identification of bacteria and archaea with mashID (https://github.com/duceppemo/mashID).</p><p dir="ltr">Contents</p><p dir="ltr">- progenomes4_2026-09-22.msh: Mash 2.3 sketches, k-mer size 21, sketch size 2000, 32,887 representative genomes, one per proGenomes species cluster, spanning 4,384 genera (536 MB). MD5: daa010ff78267f365aef8d9a05eb9b02</p><p dir="ltr">- progenomes4_2026-09-22.metadata.tsv: one line per reference with assembly accession, organism name and NCBI TaxID (current NCBI taxonomy, retrieved with NCBI Datasets on 2026-09-22), 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">The proGenomes 4 representatives multi-fasta (pg4_genomes_representatives.fna.gz, 45.9 GB, dated 2025-11-11) was split into one file per assembly accession, organism names and TaxIDs were fetched for every accession from NCBI Datasets, and the genomes were sketched with make_mashID_db (references shorter than 100 kb excluded; none were). No dereplication was applied since proGenomes representatives are already one genome per species cluster. Sketch size 2000 keeps the database at 536 MB; a sketch size of 10000 gave a 2.6 GB file with no practical gain for species-level screening. Reproducible with</p><p dir="ltr">scripts/build_progenomes_db.sh in the mashID repository.</p><p dir="ltr">Usage</p><p dir="ltr">mashID -i reads/ -o results -d progenomes4_2026-09-22.msh</p><p dir="ltr">Keep the .metadata.tsv file next to the .msh file. Identities against a single representative per species are typically 0.95 to 0.99 for a sample of that species; use a genus- or family-specific mashID database for finer resolution.</p><p dir="ltr">Please cite proGenomes when using this database (Fullam et al., proGenomes3, Nucleic Acids Research 2023, and the proGenomes 4 release).</p> 2026-09-22T20:31:31Z Dataset Dataset 10.6084/m9.figshare.33968806.v1 https://figshare.com/articles/dataset/proGenomes_4_representative_genomes_database_for_mashID_-_2026-09-22/33968806 CC BY 4.0