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Local bioinformatics databases

Hydra keeps large, widely used reference databases under /scratch/dbs, so that each user does not download a copy. Email [email protected] to request a database.

Old versions are not kept

An update removes the previous copy. If your pipeline depends on a particular version, record the version from the README in the database directory.

/scratch/dbs/blast

This directory holds the databases for BLAST and diamond.

/scratch/dbs/blast
└── v5/            # v5 of the nr, nt, refseq_protein, swissprot, taxdb databases
    ├── README     # download commands, database and version information
    ├── mito/      # v5 of mito
    └── core_nt    # v5 of core_nt

Loading bio/blast sets BLASTDB to /scratch/dbs/blast/v5, so -db nt finds the local copy. See BLAST.

/scratch/dbs/dfam

/scratch/dbs/dfam
├── README           # database and version information
├── 3.8/             # Dfam FamDB 3.8
└── 3.9/             # Dfam FamDB 3.9

Local copies of the Dfam FamDB transposable-element partitions, used by the RepeatMasker modules: Dfam 3.8 for RepeatMasker 4.1.x, from https://www.dfam.org/releases/Dfam_3.8/families/FamDB/, and Dfam 3.9 for RepeatMasker 4.2.x, from https://www.dfam.org/releases/Dfam_3.9/families/FamDB/. README.txt in each directory lists the taxonomic grouping of the partitions. In the RepeatMasker installations under /share/apps/bioinformatics/repeatmasker, these .h5 files are linked into share/RepeatMasker/Libraries/famdb.

/scratch/dbs/kraken

/scratch/dbs/kraken
├── README         # database and version information
├── core_nt/       # "very large collection, inclusive of GenBank, RefSeq, TPA and PDB"
└── standard/      # "RefSeq archaea, bacteria, viral, plasmid, human, UniVec_Core"

Local copies of the standard and core_nt Kraken 2 indexes from https://benlangmead.github.io/aws-indexes/k2.

/scratch/dbs/kraken-uniq

/scratch/dbs/kraken-uniq
├── README         # database and version information
└── standard/      # "archaea, bacteria, viral, human, UniVec_Core"

A local copy of the standard KrakenUniq index from https://benlangmead.github.io/aws-indexes/k2.

Last updated 2026-10-04