proGenomes 4 representative genomes database for mashID - 2026-09-22

<p dir="ltr">Mash sketch database of the proGenomes 4 representative genomes (progenomes.embl.de) for species-level identification of bacteria and archaea with mashID (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).