Reference DataΒΆ
We keep a number of reference data sets available on Katana at /data/ so that we don't accidentally - for instance - end up with 150 copies of the Human Genome in user's home directories.
As these are reference data, they don't change often and we can update them as necessary.
| Directory | Description | Update Schedule | URL |
|---|---|---|---|
| annovar | Reference datasets that come with software installation. | Installed when software is installed. | annovar.openbioinformatics.org |
| antismash | Reference files and commands for antismash version 4.2.0 | Version specific database installed when software is installed | antismash.secondarymetabolites.org |
| blast | NCBI nr, nt, refseq_genomic and refseq datasets | Updated on release 6 times a year | www.ncbi.nlm.nih.gov/refseq |
| blastv5 | Version 5 of NCBI nr, nt, refseq_genomic and refseq datasets. | Updated on release 6 times a year. | www.ncbi.nlm.nih.gov/refseq |
| diamond | Diamond reference databases for versions 0.8.38, 0.9.10, 0.9.22 and 0.9.24. Database format periodically changes. | Updated when NCBI nr databases are updated. | ab.inf.uni-tuebingen.de/software/diamond |
| gtdbtk | Version specific database installed when software is installed. | ||
| gtex | Genotype-Tissue Expression project, comprehensive resource to study tissue-specific gene expression and regulation | Please contact the [Oates lab](mailto:e.oates@unsw.edu.au) for access to a large set of GTEx datathat is not publicly available. | https://gtexportal.org/home/ |
| hapcol | Reference datasets that come with software installation. | Installed when software is installed. | hapcol.algolab.eu |
| hg19 | Human reference genome hg19 (GRCh37). | Fixed reference. Never updated. | www.ncbi.nlm.nih.gov/grc |
| interproscan | Reference datasets for InterProScan versions 5.20-59.0 and 5.35-74.0 | Version specific database installed when software is installed. | www.ebi.ac.uk/interpro |
| itasser | Rererence datasets for I-TASSER plus link to current nr database. | Version specific databases installed when software is installed plus link to nr database (see blast above). | zhanglab.ccmb.med.umich.edu/I-TASSER |
| kaiju | Reference databases for all versions of Kaiju. Same databases for all versions. | Databases installed when software is installed. | kaiju.binf.ku.dk |
| matam | Reference databases for all MATAM versions. | Version specific database installed when software is installed. | github.com/bonsai-team/matam |
| megan | Reference databases for all MEGAN versions. | Version specific database installed when software is installed. | ab.inf.uni-tuebingen.de/software/megan6 |
| repeatmasker | Reference datasets for RepeatMasker version 4.0.7 | Version specific database installed when software is installed. | www.repeatmasker.org |
| sra | Sequence Read Archive, repository of high throughput sequencing data | https://www.ncbi.nlm.nih.gov/sra | |
| trinotate | Reference databases for all versions of Kaiju. Same databases for all versions. | Databases installed when software is installed. | trinotate.github.io |