Reference Data¶
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 (e.oates@unsw.edu.au) for access to a large set of GTEx datathat is not publicly available. |
|
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 |
||
trinotate |
Reference databases for all versions of Kaiju. Same databases for all versions. |
Databases installed when software is installed. |
trinotate.github.io |