Databases

Databases

Any Mash sketch database works with mashID. Databases are stored outside the package and outside the repository.

Pre-built databases

mashID_download_db                    # list databases and whether they are installed
mashID_download_db mycobacteriaceae   # download one (MD5-verified)
mashID_download_db --all --dir /db    # download everything somewhere else

Name	Content	Size
mycobacteriaceae (default)	Mycobacteriaceae (NCBI taxon 1762): 16,189 GenBank assemblies as of 2026-09-22, dereplicated per species at 99.9% identity to 3534 references, NCBI TaxIDs for all. k=21, s=10000. Ships with its metadata sidecar. Figshare	284 MB
mycobacteriaceae-2025	The previous Mycobacteriaceae database (2025-02-20): 3309 references, k=21, s=1000, no TaxIDs. Kept for reproducibility. Figshare	27 MB
listeria	Listeria (NCBI taxon 1637): 7453 RefSeq assemblies as of 2026-09-22, dereplicated per species at 99.9% identity to 1441 references covering 42 species and subspecies, NCBI TaxIDs for all. k=21, s=10000. Ships with its metadata sidecar. Figshare	116 MB
listeria-2025	The previous Listeria database (2025-02-18), no TaxIDs. Kept for reproducibility. Figshare	46 MB
progenomes3	proGenomes v3 representative genomes, all bacteria and archaea. Figshare	331 MB
refseq_bacteria	RefSeq bacteria as of 2023-01-19, dereplicated at 99% identity. Figshare	653 MB

Databases live in $MASHID_DB_DIR if set, else $XDG_DATA_HOME/mashID/db (~/.local/share/mashID/db). Pass a name (-d listeria) or a path (-d /db/x.msh) to mashID. A metadata sidecar (see below) is generated right after download.

Building your own

make_mashID_db -i /path/to/genomes -o /path/to/db -p my_database -s 10000 -k 21 -t 16
# -> /path/to/db/my_database.msh and /path/to/db/my_database.metadata.tsv

Option	Description
-i PATH	Directory searched recursively for .fna/.fa/.fasta[.gz], or a text file listing one genome path per line.
-o DIR, -p NAME	Output directory and database name (.msh is appended).
-s 10000	Sketch size. 10000 is recommended for species-level identification.
-k 21	K-mer size (1–32).
--min-length 100000	Exclude references shorter than this; use 0 for plasmid or viral collections.
--metadata FILE	TSV/CSV with Accession, Organism and optionally TaxID columns.
--assembly-report FILE.jsonl	assembly_data_report.jsonl from an NCBI datasets download genome archive.
--annotate DB.msh	Only (re)write the metadata sidecar of an existing database.
--check DB.msh	Report quality issues of a database: references shorter than --min-length, unparsed organism names, missing TaxIDs, species listed under several genera (synonyms), single-reference organisms.

scripts/build_mycobacteriaceae_db.sh in the repository shows a full workflow: download all NCBI genomes of a taxon with datasets, dereplicate them per species with Assembly-dereplicator, and sketch the database.

Checking a database

make_mashID_db --check /path/to/db.msh

Run this on any database before trusting it. On the 2025 Mycobacteriaceae database (mycobacteriaceae-2025) it reports seven references under 100 kb (partial records that would otherwise become false top hits), no TaxIDs, and 40 species that appear under two or three genera because of the Mycobacterium → Mycolicibacterium / Mycobacteroides / Mycolicibacter reclassification. The last point matters: mashID counts Mycobacterium abscessus and Mycobacteroides abscessus as different organisms, so a sample may show a spurious "Possible mixture" between the two names. A sidecar built from NCBI's assembly report (--annotate --assembly-report) or a curated --metadata table harmonises them.

Provenance and known issues of the pre-built databases

Database	Built	Source and filters	Known issues
mycobacteriaceae	2026-09-22	scripts/build_mycobacteriaceae_db.sh: all 16,189 GenBank assemblies of taxon 1762 (atypical excluded) via NCBI Datasets, binned by species from the assembly report, dereplicated per species at Mash distance 0.001 with Assembly-dereplicator 0.3.2 (M. tuberculosis: 211 of 8722 kept), references < 100 kb excluded, sketched k=21, s=10000. 3534 references; names and TaxIDs from the assembly report, strain text removed.	--check reports one species under two genus spellings ([Mycobacterium] chelonae, NCBI's own naming). MTBC members are not separable (see Interpreting results).
mycobacteriaceae-2025	2025-02-20	All NCBI assemblies of taxon 1762 from the datasets web table (26,101), renamed and binned by the species in the first header, dereplicated per species at Mash distance 0.001 with Assembly-dereplicator 0.3.2, sketched k=21, s=1000. 3309 references.	Seven references < 100 kb; names parsed from headers, so genus synonyms are not merged; no TaxIDs; s=1000 gives identities in steps of 0.001. Superseded by mycobacteriaceae.
listeria	2026-09-22	scripts/build_mycobacteriaceae_db.sh with ASSEMBLY_SOURCE=RefSeq and taxon 1637: all 7453 RefSeq assemblies (atypical excluded; GenBank's 79,000 are mostly redundant L. monocytogenes), binned by species from the assembly report, dereplicated per species at Mash distance 0.001 (L. monocytogenes: 892 kept), references < 100 kb excluded, sketched k=21, s=10000. 1441 references with NCBI names and TaxIDs.	--check reports no issues. Validated on Nanopore L. ivanovii subsp. londoniensis and L. monocytogenes reads and an assembly.
listeria-2025	2025-02-18	All NCBI Listeria assemblies, dereplicated as above.	Names parsed from headers; no TaxIDs. Superseded by listeria.
progenomes3	2023-03	proGenomes v3 representative genomes, sketched from the proGenomes fasta.	Header format differs from NCBI's; names come from the sidecar generated on first use, check them with --check.
refseq_bacteria	2023-01-19	RefSeq bacteria, dereplicated at 0.01.	Large (653 MB); three years old.

The metadata sidecar

<database>.metadata.tsv sits next to the .msh file and holds, for every reference: Accession, Organism, TaxID, Length, Hashes, Source_File, Description.

It is the source of Identification and TaxID in the outputs, and of the reference lengths used by --min-ref-length. Organism names come from, in order of preference:

1. --metadata FILE: your own table.
2. --assembly-report: NCBI's report, which carries organism names and TaxIDs for every accession.
3. The first fasta header of each genome, parsed for genus, species and infraspecific ranks (NZ_CP060409.1 Mycolicibacterium fortuitum strain W4 chromosome → Mycolicibacterium fortuitum).

Accessions are recognised in file names (GCF_000195955.2_ASM19595v2_genomic.fna.gz → GCF_000195955.2). If a database has no sidecar, mashID builds one on first use from mash info, and writes it next to the database when the directory is writable. To add or refresh a sidecar, including for downloaded databases:

make_mashID_db --annotate /path/to/db.msh --assembly-report assembly_data_report.jsonl

Choosing a sketch size

The pre-built Mycobacteriaceae database uses s=1000, which resolves species but yields coarse identities (steps of 0.001). For a custom database aimed at close relatives, s=10000 is worth the tenfold larger file: identities become finer and the shared-hash counts more informative.