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
salmonella	Salmonella (NCBI taxon 590): 21,133 RefSeq assemblies as of 2026-09-22, binned by subspecies and dereplicated to 1442 references covering S. bongori and all six S. enterica subspecies, NCBI TaxIDs for all. k=21, s=10000. Ships with its metadata sidecar. Species and subspecies level: the serovar in a reference name is that of the nearest reference, not a serotype determination; use SeqSero2 or SISTR for serotyping. Figshare	116 MB
brucella	Brucella (NCBI taxon 234, including the former Ochrobactrum species): all 1995 GenBank assemblies as of 2026-09-22, dereplicated per species at Mash distance 0.0003 to 387 references covering 29 species, NCBI TaxIDs for all. k=21, s=10000. Ships with its metadata sidecar. Held-out concordance 93.4%; the classical species are host-adapted lineages 0.2 to 0.5% apart, so their calls are nearest-reference calls and biovars are not resolved. Figshare	31 MB
escherichia	Escherichia and Shigella (NCBI taxa 561 and 620): 57,146 RefSeq assemblies as of 2026-09-22, dereplicated to 4503 references (E. coli 3316, five other Escherichia species, four Shigella species), NCBI TaxIDs for all. k=21, s=10000. Ships with its metadata sidecar. Held-out concordance 96.4% at species level; S. boydii, S. dysenteriae and S. flexneri share lineages and are not reliably separated from each other, nor enteroinvasive E. coli from Shigella: use ShigaTyper or ShigEiFinder. Figshare	362 MB
refseq_viral	All 19,625 viral genomes and genome segments of NCBI RefSeq release 237 (6427 phages), current ICTV species names and TaxIDs from the GenBank flat files. k=21, s=2000. Ships with its metadata sidecar. Median reference 6.9 kb, so mashID applies no reference-length filter. For virus identification and for prophage or viral contamination detection in any sample. Figshare	304 MB
progenomes4	proGenomes 4 representative genomes: 32,887 species-cluster representatives across 4384 genera of bacteria and archaea, current NCBI names and TaxIDs for all. k=21, s=2000. Ships with its metadata sidecar. For species-level screening of anything. Figshare	536 MB
progenomes3	proGenomes v3 representative genomes (2023), names parsed from headers. Superseded by progenomes4. 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_taxon_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.

Validating a database on held-out genomes

scripts/validate_db_heldout.py <build_dir> <db.msh> screens genomes that the build downloaded but did not keep (dropped by the bin cap or by dereplication) and reports, per species, how often mashID returns the NCBI name, how often a note fired, and every mismatch. Run it after each build; the numbers in the provenance table above come from it.

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_taxon_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). Two references are mislabelled at NCBI and are corrected in curation/label_corrections.tsv: GCA_013697125.1 ("Mycobacterium canetti") is M. tuberculosis variant bovis, and GCA_025822535.1 ("Mycolicibacterium goodii") is M. wolinskyi. Databases downloaded before this was found carry the deposited names; apply the corrections with scripts/apply_label_corrections.py.
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_taxon_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.
salmonella	2026-09-22	scripts/build_taxon_db.sh with ASSEMBLY_SOURCE=RefSeq BIN_RANK=subspecies MAX_BIN=3000 and taxon 590: all 21,133 RefSeq assemblies (GenBank's 630,000 are mostly redundant), binned by subspecies, each bin capped at 3000 keeping complete genomes first, dereplicated per bin at Mash distance 0.001, assemblies named only "Salmonella sp." excluded, sketched k=21, s=10000. 1442 references with NCBI names and TaxIDs.	Nearest-reference serovars appear in names but Mash does not serotype: serovars are defined by three loci, several are polyphyletic, and rare ones have few references. --check reports no issues. Validated on SKESA assemblies and MiSeq reads of S. enterica.
brucella	2026-09-22	scripts/build_taxon_db.sh with ASSEMBLY_SOURCE=GenBank EXCLUDE_SP=1 DEREP_DISTANCE=0.0003 and taxon 234: all 1995 GenBank assemblies, binned by species, dereplicated per species at Mash distance 0.0003 (0.001 left only 21 B. melitensis and 9 B. suis references and scored 90.7% held-out; the classical species are only 0.2 to 0.5% apart), "sp." bin excluded, sketched k=21, s=10000. 387 references.	Held-out validation on 226 genomes: 93.4%; B. abortus 29/30, B. melitensis 29/30, B. suis 28/30, B. canis, B. ovis, B. ceti, B. pinnipedialis, B. microti, B. neotomae 100%. Misses match another species at > 0.9995, including a submission batch deposited as B. intermedia identical to B. ciceri. For genera whose species are this close, set DEREP_DISTANCE below the inter-species distance.
escherichia	2026-09-22	scripts/build_taxon_db.sh with ASSEMBLY_SOURCE=RefSeq MAX_BIN=5000 EXCLUDE_SP=1 and taxa 561,620: all RefSeq Escherichia (53,845) and Shigella (3,301) assemblies, binned by species, each bin capped at 5000 keeping complete genomes first (for E. coli that is the 5595 complete genomes), dereplicated per bin at Mash distance 0.001, "sp." bins excluded, sketched k=21, s=10000.	Validated with scripts/validate_db_heldout.py on 251 genomes left out of the database: 96.4% species concordance, 100% for every Escherichia species but E. coli (28/30, both misses matching S. sonnei at 0.99); the other misses are Shigella genomes matching another Shigella species at > 0.999 identity, a labelling matter Mash cannot resolve. Complete genomes over-represent clinical and outbreak lineages.
refseq_viral	2026-09-28	scripts/build_virus_db.sh: the viral division of RefSeq release 237 from the NCBI FTP release files, split into one file per record, names and TaxIDs from the GenBank flat file (scripts/refseq_gbff_metadata.py), sketched k=21, s=2000, no length filter, no dereplication (one reference per species or segment). 19,625 references.	Names are RefSeq's ORGANISM field, i.e. ICTV species names ("limnipivirus B1"); the familiar name is in Description. Segmented viruses appear as separate segments. Divergent viruses without a close RefSeq relative are not detected at k=21. Tested: RefSeq phages self-match at identity 1; two S. Infantis assemblies show a complete Salmonella phage MET_P1_103_31 prophage at 0.9996; M. bovis assemblies and reads give no hit.
progenomes4	2026-09-22	scripts/build_progenomes_db.sh: the proGenomes 4 representatives multi-fasta (45.9 GB) split per assembly accession, names and TaxIDs fetched from NCBI Datasets for every accession, sketched k=21, s=2000, no dereplication (one genome per species cluster already).	Single representative per species, so identities of 0.95 to 0.99 are normal; use a group-specific database for finer resolution. --check reports 2230 epithets shared across genera and 91 references named "bacterium" or similar: expected at this scale, not synonyms.
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. Superseded by progenomes4.
refseq_bacteria	2023-01-19	RefSeq bacteria, dereplicated at 0.01.	Large (653 MB); three years old.

scripts/build_virus_db.sh builds a database of every RefSeq viral genome from the NCBI RefSeq release files, with names and TaxIDs from the GenBank flat files (scripts/refseq_gbff_metadata.py).

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

Organisms the database cannot separate

Whether two organisms can be told apart is a property of the database, not of a sample: the same two references are the same distance apart in every run. Computing it once makes the per-sample annotation free, and correct whether or not winner-take-all is in use — unlike --ambiguity-margin, which cannot see a close relative under winner-take-all at all (see Outputs).

make_mashID_db --confusable /path/to/db.msh -t 16          # writes db.confusable.tsv
make_mashID_db --confusable /path/to/db.msh --confusable-distance 0.002

For each reference the table records the closest reference of every other organism within --confusable-distance (default 0.005, matching --ambiguity-margin), nearest pair first:

Accession        Organism                                  Confusable_Organism             Distance  Nearest_Accession
GCA_025821985.1  Mycobacterium timonense                   Mycobacterium bouchedurhonense  0.000041  GCA_025822125.1
GCA_013697125.1  Mycobacterium tuberculosis variant bovis  Mycobacterium tuberculosis      0.000972  GCA_021325765.1

mashID picks the sidecar up automatically and notes affected calls; --db-confusable points at a different table. Runs that finished before the table existed do not have to be screened again:

scripts/reannotate_summary.py /path/to/results --dry-run   # then without --dry-run

rebuilds their summary files from the per-sample tables and the current sidecars, which is also how to apply a corrected organism name to results that predate the correction. Names are compared as organisms, not as strings, so Genus sp. placeholders and the same epithet under two genera (Mycobacterium/Mycobacteroides abscessus) are not reported as conflicts.

A name and a rank below it are reported, which is two thirds of the rows for mycobacteriaceae (1306 of 1993). Some of those pairs are the most important thing the table has to say — M. tuberculosis against M. tuberculosis variant bovis is the second row above — while others are merely redundant, such as Mycobacteroides abscessus against M. abscessus subsp. abscessus. The two are the same shape and cannot be told apart without a taxonomy, so both are kept: a redundant line in a note costs little, and suppressing the shape would hide the bovis case.

It is an all-pairs comparison, so cost grows with the square of the reference count: 3,534 references of mycobacteriaceae take under two minutes and 850 MB and flag 945 references, but a database with hundreds of thousands of references is a different proposition. This is why it is a separate step rather than part of every build.

Read the table top-down and it doubles as the sharpest mislabel detector available: a reference named for one species sitting a hair from another species' references is either a genuinely inseparable pair or a bad label. Both mislabelled mycobacteriaceae references were in the first 20 of 2,102 rows, GCA_025822535.1 at rank 4.

Correcting a mislabelled reference

Some assemblies are deposited under the wrong organism name, and a reference named for a species it does not belong to misidentifies every sample of the species it really is. Because Mash's winner-take-all strategy credits each shared hash to a single reference, such a reference only has to win by a few hashes to take them all, which also pushes the correct references far down the hit list: a runner-up at a much lower identity is not evidence that it matched poorly.

NCBI's own ANI check is where to start looking, but it does not settle the question on its own. The average_nucleotide_identity block of a NCBI Datasets assembly report carries match_status:

• species_match — the best-matching type assembly is the declared species.
• below_threshold_match — the best match is the declared species but below the species threshold, usually a divergent or undescribed lineage rather than a mislabel.
• below_threshold_mismatch — common and usually benign where species sit above 98% ANI or the declared species has no type assembly, as across the M. tuberculosis complex.
• mismatch — the best-matching type assembly is a different species. Worth investigating, though most hits are genus reclassifications (Mycobacterium → Mycolicibacterium) or reciprocal synonym pairs: of 3,534 references in mycobacteriaceae, 38 were flagged and 2 were real.

Confirm before relabelling, with evidence that suits the group. ANI against the type strain of both candidate species decides it for most genera; within the M. tuberculosis complex, where ANI is uninformative, the regions of difference do (GCA_013697125.1 was settled by the bovis-exclusive RD4 deletion). Record the correction, the deposited name and the evidence in curation/label_corrections.tsv, then apply it.

On an existing database, rewrite the sidecar and bins.tsv in place — no re-sketching, and --dry-run first:

scripts/apply_label_corrections.py curation/label_corrections.tsv \
    ~/.local/share/mashID/db/<db>.metadata.tsv <build_dir>/bins.tsv

Identification and TaxID are then correct. Description comes from the reference's own fasta header by way of the sketch, so it keeps the deposited name until the database is rebuilt.

On a rebuild, pass the same file to both steps. The binner needs it too: binning is what decides which genomes a reference is dereplicated against, and a mislabelled genome put in the wrong bin is compared only with the species it is named for, so it survives as a near-duplicate of the cluster it actually belongs to — which is how both mycobacteriaceae references got in.

scripts/bin_by_species.py assembly_data_report.jsonl ncbi_dataset/data binned/ \
    --corrections curation/label_corrections.tsv
make_mashID_db -i binned/ -o /path/to/db -p my_database \
    --assembly-report assembly_data_report.jsonl \
    --metadata curation/label_corrections.tsv

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.