Databases
We host several bioinformatics databases on the Center for High Throughput Computing’s HTC cluster under the /projects folder.
The projects folder data can be accessed in jobs by specifying: Requirements == (HasCHTCProjects) in the submit file.
Path to bioinformatics databases on CHTC
| Database | Path | For software | Database version | Purposes | Folder Size | Number of items | Link to software documentation | Notes |
|---|---|---|---|---|---|---|---|---|
| AntiSMASH | /projects/bacteriology_tran_data/antismash_db | Antismash | Genome annotation | 7GB | 144 | |||
| Bakta V6 | /projects/bacteriology_tran_data/bakta/v6/db | Bakta | Genome annotation | 83GB | 213 | https://github.com/oschwengers/bakta | ||
| Blast NR database | /projects/bacteriology_tran_data/blast/02.2026 | BLAST | Blast database (protein) | 1TB | 1.138 | https://ftp.ncbi.nlm.nih.gov/blast/db/ | ||
| CheckM2 | /projects/bacteriology_tran_data/checkm2_database/CheckM2_database | CheckM2 | Genome completeness and contamination checker | 3GB | 1 | https://github.com/chklovski/CheckM2?tab=readme-ov-file#database | ||
| CheckV DB v1.5 | /projects/bacteriology_tran_data/checkV_db/checkv-db-v1.5 | CheckV | Genome completeness and contamination checker for phages | 6.4GB | 94 | https://portal.nersc.gov/CheckV/ | ||
| DefenseFinder v2.0 | /projects/bacteriology_tran_data/defense_finder_v2.0.0_models | DefenseFinder | Phage defense and anti-defense systems identification | 315MB | 2.640 | |||
| Eggnog db 5.0.2, including pfams and mmseqs | /projects/bacteriology_tran_data/eggnog | EGGNOG-mapper | Genome annotation against multiple databases | 67GB | 26 | http://eggnog5.embl.de/download/eggnog_5.0/ | ||
| GTDB-tk database v220 | /projects/bacteriology_tran_data/gtdbtk_v220 | GTDB-tk V2.4.0 to current | Genome taxonomy | 106G | 241.862 | https://ecogenomics.github.io/GTDBTk/installing/index.html | ||
| GTDB-tk database v226 | /projects/bacteriology_tran_data/gtdbtk_v226 | GTDB-tk V2.4.1 to current | Genome taxonomy | 138G | 307.538 | https://ecogenomics.github.io/GTDBTk/installing/index.html | ||
| kraken DB Standard | /projects/bacteriology_tran_data/kraken2_db_standard_20260226 | Kraken2 | Reads taxonomy | 173GB | 18 | https://benlangmead.github.io/aws-indexes/k2 | ||
| minikraken_8GB_20200312 | /projects/bacteriology_tran_data/kraken_db/minikraken_8GB_20200312/ | Kraken2 | Reads taxonomy | 7.5GB | 10 | https://benlangmead.github.io/aws-indexes/k2 | ||
| Kraken DB Plus FPF | /projects/bacteriology_tran_data/kraken_db_PlusFPF | Kraken2 | Reads taxonomy | 368GB | 18 | https://benlangmead.github.io/aws-indexes/k2 | ||
| Kaiju DB nr | /projects/bacteriology_tran_data/kaiju_db/kaiju_db_nr_2024-08-25 | Kaiju | Reads taxonomy | 269GB | 4 | https://kaiju.binf.ku.dk/ | ||
| GTDB-tk database v232 | /projects/bacteriology_tran_data/gtdbtk_v232 | GTDB-tk v.2.7.0 to current | Genome taxonomy | 339GB | 200.224 | https://ecogenomics.github.io/GTDBTk/installing/index.html | ||
| uniref100 | /projects/bacteriology_tran_data/uniref100_2026-01-28/ | Blastp | Blast database (protein) | 534GB | 260 | https://www.uniprot.org/help/downloads | Uniref100 (https://www.uniprot.org/help/downloads) with BlastDB build. | |
| Database | Path | For software | Database version | Purposes | Folder Size | Number of items | Link to software documentation | Notes |
Would you like to use these databases in your compute jobs?
You can use these databases directly in your CHTC HTC compute jobs!
To get started, visit https://chtc.cs.wisc.edu/uw-research-computing/form.html to request an account.
Also check out our Youtube channel for a 3 part series on how to use CHTC for bioinformatics jobs!