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.
| Database | Path | For software | Version | Purposes | Folder Size | Number of items | Link to software documentation |
| 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 | ||
| Blast NR database | /projects/bacteriology_tran_data/blast/02.2026 | BLAST | 02-2026 | Blast database (protein) | 1TB | 1138 | |
| CheckM2 | /projects/bacteriology_tran_data/checkm2_database/CheckM2_database | CheckM2 | Genome completeness and contamination checker | 3GB | 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 | 1.5 | 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 | 2 | Phage defense and anti-defense systems identification | 315MB | ||
| Eggnog db 5.0.2, including pfams and mmseqs | /projects/bacteriology_tran_data/eggnog | EGGNOG-mapper | 5.0.2 | 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 | v220 | Genome taxonomy | 106G | 241862 | 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 | v226 | Genome taxonomy | 138G | https://ecogenomics.github.io/GTDBTk/installing/index.html | |
| kraken DB Standard | /projects/bacteriology_tran_data/kraken2_db_standard_20260226 | Kraken2 | kraken2_db_standard_20260226 | Reads taxonomy | 173GB | https://benlangmead.github.io/aws-indexes/k2 | |
| minikraken_8GB_20200312 | /projects/bacteriology_tran_data/kraken_db/minikraken_8GB_20200312/ | Kraken2 | minikraken Mar 27 2020 | Reads taxonomy | 7.5GB | https://benlangmead.github.io/aws-indexes/k2 | |
| Kraken DB Plus FPF | /projects/bacteriology_tran_data/kraken_db_PlusFPF | Kraken2 | 20250714 | Reads taxonomy | 368GB | https://benlangmead.github.io/aws-indexes/k2 | |
| Kaiju DB nr | /projects/bacteriology_tran_data/kaiju_db/kaiju_db_nr_2024-08-25 | Kaiju | nr_2024-08-25 | Reads taxonomy | 269GB | https://kaiju.binf.ku.dk/ | |
| GTDB-tk database v232 | /projects/bacteriology_tran_data/gtdbtk_v232/release232 | GTDB-tk v.2.7.0 to current | v232 | Genome taxonomy | 94GB | https://ecogenomics.github.io/GTDBTk/installing/index.html | |
| uniref100 | /projects/bacteriology_tran_data/uniref100_2026-01-28/ | Blastp | version 2026-01-2028 | Uniref100 (https://www.uniprot.org/help/downloads) with BlastDB build. | https://www.uniprot.org/help/downloads |
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.