Difference between revisions of "Reference Data"
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| + | [[Category:Reference Data]]__NOTOC__ | ||
UFRC maintains a repository of reference data that can be accessed by all HiPerGator users. The primary purposes of this repository are researcher convenience, efficient use of filesystem space, and cost savings. We are happy to download and build reference datasets and configure applications installed on HiPerGator to automatically make use of the available reference data. Having UFRC host common reference data means that a research group does not have to use their Blue or Orange quota to host redundant copies of common reference data. | UFRC maintains a repository of reference data that can be accessed by all HiPerGator users. The primary purposes of this repository are researcher convenience, efficient use of filesystem space, and cost savings. We are happy to download and build reference datasets and configure applications installed on HiPerGator to automatically make use of the available reference data. Having UFRC host common reference data means that a research group does not have to use their Blue or Orange quota to host redundant copies of common reference data. | ||
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* [[BLASTDB|NCBI Blast Databases]] | * [[BLASTDB|NCBI Blast Databases]] | ||
* [[SnpEff Databases]] | * [[SnpEff Databases]] | ||
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| + | Many other application specific references are located in <code>/data/reference</code>. | ||
==Raw Genomic Data== | ==Raw Genomic Data== | ||
| − | * [http://gigadb.org/dataset/200001 3k Rice genomes] - reference/genomes/rice3k, fastq format | + | * [http://gigadb.org/dataset/200001 3k Rice genomes] - /data/reference/genomes/rice3k, fastq format |
| + | * [https://www.internationalgenome.org/data/ 1000 Genomes Data Releases] - /data/reference/1000genomes | ||
| + | * [https://www.girinst.org/repbase/ RepBase] - /data/reference/repbase | ||
| + | * [https://bfd.mmseqs.com/ BFD] - /data/reference/bfd | ||
| + | * [https://www.uniprot.org/help/uniref Uniref30] - /data/reference/uniref30 | ||
| + | * [https://www.uniprot.org/help/uniref Uniref90] - /data/reference/uniref90 | ||
| + | * [https://www.ebi.ac.uk/metagenomics/ MGnify] - /data/reference/mgnify | ||
| + | * [http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/ pdb70] - /data/reference/pdb70 | ||
| + | * Various other references - /data/reference/fasta | ||
==AI Reference Datasets and Models== | ==AI Reference Datasets and Models== | ||
| − | A variety of reference machine learning and AI datasets are located in <code>/data/ai</code>. Browse the [[AI Reference Datasets|catalog of all available AI reference datasets]] to learn more. | + | A variety of reference machine learning and AI datasets are located in <code>/data/ai</code>. You may need to use the full path /blue/data/ai for applications to find the files. Browse the [[AI Reference Datasets|catalog of all available AI reference datasets]] to learn more. |
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| + | * [https://mediatum.ub.tum.de/1474000 SEN12MS] - curated dataset of georeferenced multi-spectral Sentinel-1 imagery for deep learning and data fusion. | ||
| + | * [https://github.com/Open-Catalyst-Project/ocp/blob/main/DATASET.md OC20 Structure to Energy and Forces (S2EF)] - /data/reference/ocp/s2ef_train_all | ||
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| + | ==Repbase Sequencing Data== | ||
| + | [https://www.girinst.org/about/repbase.html Repbase] is 'a database of representative repetitive sequences from eukaryotic species. Repbase is being used worldwide as the reference standard for annotating the presence of repetitive DNA in genomic data.' | ||
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| + | A university-wide license for Repbase data is currently in effect for the University of Florida. It will expire on March 22nd, 2022. | ||
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| + | Repbase data can be [https://www.girinst.org/server/RepBase/index.php downloaded] from UF IP Addresses for use on local computers. | ||
| − | + | We maintain copies of Repbase releases in sub-directories under /data/reference/repbase on HiPerGator and also configure RepeatMasker and Maker applications to use Repbase data automatically. | |
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Latest revision as of 19:55, 2 November 2023
UFRC maintains a repository of reference data that can be accessed by all HiPerGator users. The primary purposes of this repository are researcher convenience, efficient use of filesystem space, and cost savings. We are happy to download and build reference datasets and configure applications installed on HiPerGator to automatically make use of the available reference data. Having UFRC host common reference data means that a research group does not have to use their Blue or Orange quota to host redundant copies of common reference data.
Use https://support.rc.ufl.edu to request either addition of reference data or to ask for an addition of a directory that you can put reference data into for shared use.
The following is not an exhaustive list of the hosted reference data. If an existing reference is missing from the list below please let us know and we will update the list.
Application-Specific Data
Many other application specific references are located in /data/reference.
Raw Genomic Data
- 3k Rice genomes - /data/reference/genomes/rice3k, fastq format
- 1000 Genomes Data Releases - /data/reference/1000genomes
- RepBase - /data/reference/repbase
- BFD - /data/reference/bfd
- Uniref30 - /data/reference/uniref30
- Uniref90 - /data/reference/uniref90
- MGnify - /data/reference/mgnify
- pdb70 - /data/reference/pdb70
- Various other references - /data/reference/fasta
AI Reference Datasets and Models
A variety of reference machine learning and AI datasets are located in /data/ai. You may need to use the full path /blue/data/ai for applications to find the files. Browse the catalog of all available AI reference datasets to learn more.
- SEN12MS - curated dataset of georeferenced multi-spectral Sentinel-1 imagery for deep learning and data fusion.
- OC20 Structure to Energy and Forces (S2EF) - /data/reference/ocp/s2ef_train_all
Repbase Sequencing Data
Repbase is 'a database of representative repetitive sequences from eukaryotic species. Repbase is being used worldwide as the reference standard for annotating the presence of repetitive DNA in genomic data.'
A university-wide license for Repbase data is currently in effect for the University of Florida. It will expire on March 22nd, 2022.
Repbase data can be downloaded from UF IP Addresses for use on local computers.
We maintain copies of Repbase releases in sub-directories under /data/reference/repbase on HiPerGator and also configure RepeatMasker and Maker applications to use Repbase data automatically.