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updated and extended Kraken 2 databases, new location #65

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Aug 25, 2025
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updated and extended Kraken 2 databases, new location #65

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13 changes: 4 additions & 9 deletions content/docs/software/sw-list/kraken.mdx
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Expand Up @@ -10,18 +10,13 @@ module avail kraken2/

## Database

There is an `nt` Kraken2 database available in a shared location. In order to use it, run
There are public Kraken2 databases (originally from https://benlangmead.github.io/aws-indexes/) available in a shared location. In order to use one of them, run

```bash
kraken2 --db /storage/brno12-cerit/projects/Bio_databases/kraken2_nt_20240530
kraken2 --db /storage/projects-du-praha/Bio_databases/kraken2/CHOSEN_DATABASE
# includes the NCBI Taxonomy database
```

```bash
# older releases:
# /storage/brno12-cerit/projects/Bio_databases/kraken2_nt_20230502
```

and request at least `mem=890gb` for `kraken2_nt_20240530` database (unless only a short query is processed with the `--memory-mapping` option) or `mem=520gb` for `kraken2_nt_20230502` database (unless only a short query is processed with the `--memory-mapping` option).
and request enough memory to contain entire database (e.g. at least `mem=900gb` for `kraken2_nt_20240530` database,please use `du -h` on database directory to get its size), unless only a short query is processed with the `--memory-mapping` option.

For optimal performance of access to this database, we recommend adding `qsub` requirement `cluster=halmir`. This selects machines with the fastest network connection to the database storage.
For fast access to the largest databases (e.g. kraken2_nt_20240530, k2_gtdb_genome_reps_20250609, k2_core_nt_20250609), we recommend adding `qsub` requirement `cluster=turin`. This selects machines with the fastest network connection to the database storage.