Databases:)

ganon build downloads and builds databases based on NCBI RefSeq and/or GenBank genomes repositories with GTDB support. For example:

# All archaeal and bacterial genomes from current RefSeq
ganon build -b refseq -g archaea bacteria -d rs_arc_bac -c -t 30

# Some days later, the database can be synced to the latest NCBI version with
ganon update -d arc_bac -t 30

• Pre-built databases are not provided. ganon build downloads and build databases easily and efficiently. That way you get the latest and most diverse data available.
  • The command generator can help you start with the build command.
• To build databases based on local/non-standard files, check the ganon build-custom command and documentation
  • Examples of commonly used (not standard) databases can be found here.

Simple ganon build command generator:)

Commonly used sub-sets:)

The table below lists the resources and time needed to build commonly used sub-sets. By the time you read this, these numbers will have increased slightly. As a rule of thumb, the more the better, so choose the most comprehensive sub-set as possible given your computational resources.

• To build smaller databases with less memory, you can apply some filters or tweak parameters. Note that there will be trade-offs in every reduction.

¹ data from 2026-06-21

² "Size" (in GB) is the final ganon database size. "Time" accounts for wall time for the build process after downloading files. The memory required for the build is approximate 1.5x the database size. Your time may vary based on internet, I/O, memory and CPU speed. 64 threads were used with an AMD EPYC 9454 48-Core Processor, using ganon v2.4.2.

|          RefSeq (2025-11-01) *        | # assemblies | # species | Size (GB) |
|---------------------------------------|--------------|-----------|-----------|
| All genomes                           | 468399       | 83798     | 299       |
| Complete genomes (CG)                 | 68639        | 27598     | 55        |
| Reference genomes (RG)                | 22862        | 22861     | 89        | 
| CG + RG                               | 85036        | 42955     | 120       | 

* archaea, bacteria, fungi and viral

|          RefSeq (2024-04-20) *        | # assemblies | # species | Size (GB) |
|---------------------------------------|--------------|-----------|-----------|
| All genomes                           | 366941       | 64616     | 215       |
| Complete genomes (CG)                 | 55114        | 24238     | 42        |
| Reference genomes (RG)                | 19890        | 19888     | 77        | 
| CG + RG                               | 69600        | 37864     | 100       | 

* archaea, bacteria, fungi and viral

|          RefSeq (2023-03-14) *        | # assemblies | # species | Size (GB) |
|---------------------------------------|--------------|-----------|-----------|
| All genomes                           | 295219       | 52781     | 160       |
| All genomes - 1 assembly/species      | 52781        | 52781     | 128       |
| Complete genomes                      | 44121        | 19715     | 35        |
| Complete genomes - 1 assembly/species | 19715        | 19715     | 29        |
| Reference genomes                     | 18073        | 18073     | 69        |

* archaea, bacteria, fungi and viral

|          GenBank (2023-03-14) *       | # assemblies | # species | Size (GB) |
|---------------------------------------|--------------|-----------|-----------|
| All genomes - 1 assembly/species      | 99505        | 99505     | 300       |
| Complete genomes                      | 92917        | 34815     | 42        |
| Complete genomes - 1 assembly/species | 34815        | 34815     | 34        |

* archaea, bacteria, fungi and viral

|                GTDB              | # assemblies | # species | Size (GB) |
|----------------------------------|--------------|-----------|-----------|
| R226                             | 731982       | 143396    | 501       |
| R220                             | 596859       | 113104    | 338       |
| R214                             | 402709       | 85205     | 260       |

Filters:)

Specific taxa:)

It is also possible to generate databases for one or more taxonomic branches with -a/--taxid, for example:

ganon build --source refseq --taxid 562 317 --threads 48 --db-prefix coli_syringae

will download and build a database for all Escherichia coli (taxid:562) and Pseudomonas syringae (taxid:317) assemblies from RefSeq.

This is also possible with --taxonomy gtdb, for example:

ganon build --db-prefix fuso_gtdb --taxid "f__Fusobacteriaceae" --source refseq genbank --taxonomy gtdb --threads 12

Top genomes/taxa:)

Select a specific number of genomes/assemblies for each taxa in the database. For example:

• --top 3 will select three assemblies for each taxonomic leaf
• --genome-updater "-A 'species:1'" will select one assembly for each species node

More infos about top assemblies.

Refined filters:)

ganon uses genome_updater to manage downloads and further specific options and filters can be provided with the paramer -u/--genome-updater, for example:

ganon build -g bacteria -t 48 -d bac_refseq --genome-updater "-A 'genus:3' -E 20230101"

will download top 3 archaeal assemblies for each genus with date before 2023-01-01. For more information about genome_updater parameters, please check the repository.

Update (ganon update):)

Default ganon databases generated with the ganon build can be updated with ganon update. This procedure will download new files and re-generate the ganon database adding new entires and removing outdated ones. This will keep the choosen database selection in sync with the latest available data.

For example, a database generated with the following command:

ganon build --db-prefix arc_cg_rs --source refseq --organism-group archaea --complete-genomes --threads 12

will contain all archaeal complete genomes from NCBI RefSeq at the time of running. Some days later, the database can be updated, fetching only new sequences added to the NCBI repository with the command:

ganon update --db-prefix arc_cg_rs --threads 12

Reproducibility:)

If you use ganon with default databases and want to re-generate it later or keep track of the content for reproducibility purposes, you can save the assembly_summary.txt file located inside the {output_prefix}_files/ directory. To re-download the exact same snapshot of files used, one could use genome_updater, for example:

genome_updater.sh -e assembly_summary.txt -f "genomic.fna.gz" -o recovered_files -m -t 12 

Reducing database size:)

False positive:)

A higher --max-fp value will generate a smaller database but with a higher number of false positive matches on classification. More details. Values between 0.001 (0.1%) and 0.3 (30%) are generally used.

k-mer and window size:)

Define how much unique information is stored in the database. More details

• The smaller the --kmer-size, the less unique they will be, reducing database size but also sensitivity in classification.
• The bigger the --window-size, the less information needs to be stored resulting in smaller databases but with decrease classification accuracy.

Top assemblies:)

RefSeq and GenBank are highly biased toward some few organisms. This means that some species are highly represented in number of assemblies compared to others. This can bias analysis towards those organisms. Choosing a certain number of top assemblies can mitigate those issues. Database sizes can also be drastically reduced without this redundancy, but "strain-level" analysis are then not possible. We recommend using top assemblies for larger and comprehensive reference sets (like the ones listed above) and use the full set of assemblies for specific clade analysis.

Database level:)

With the --level parameter one can define the final taxonomic level of the database. It can be a taxonomic rank ['species', 'genus', ...], 'leaves' for taxonomic leaves or 'assembly' for a assembly/strain based analysis. The default value in ganon build is species but if you don't need species resolution you can set to a less specific rank (e.g. genus). That will generate smaller databases.

Split databases:)

Ganon allows classification with multiple databases in one level or in an hierarchy (More details). This means that databases can be built separately and used in any combination as desired. There are usually some benefits of doing so:

• Smaller databases when building by organism group, for example: one for bacteria, another for viruses, etc.
• Easier to maintain and update.
• Extend use cases and avoid misclassification due to contaminated databases.
• Use databases as quality control, for example: remove reads matching one database of host or vectors (check out ganon report --skip-hierarchy).