Public Datasets
RCD hosts a number of widely used publicly available datasets on Indigo,
available at /datasets. This eliminates the need for users to consume space in
their home, project or scratch spaces.
Please submit a ticket to request changes/additions to this list.
| Dataset | Path | Description |
|---|---|---|
| AlphaFold2 | /datasets/alphafold | Genetic databases for running AlphaFold2 inferences. Use --data_dir=/datasets/alphafold when running your model. For details about running AlphaFold2, please refer to our software page. |
| AlphaFold3 | /datasets/alphafold3 | Genetic databases for running AlphaFold3 inferences. Use --data_dir=/datasets/alphafold3 when running your model. For details about running AlphaFold3, please refer to our software page. |
| BLAST | /datasets/blast/db | nt,nr,refseq_protein,refseq_rna,swissprot databases for use with NCBI BLAST+. Put export BLASTDB=/datasets/blast/db at the beginning of your batch scripts or in ~/.bashrc to use these databases. For details about running Blast, please refer to our software page. |
| CheckM2 | /datasets/CheckM2_database/ | CheckM2 uses machine learning to assess the quality of metagenome-derived genome bin. For details about running CheckM2, please refer to our software page. |
| GTDB-Tk | /datasets/GTDB-Tk/ | GTDB-Tk assigns taxonomic classifications to bacterial and archaeal genomes. For details about running GTDB-Tk, please refer to our software page. |
| iGenomes | /datasets/igenomes | Reference genome sequences download from AWS iGenomes. For use in nf-core Nextflow pipelines, see the usage instructions |
| ImageNet | /datasets/imagenet | The largest data set for visual object recognition software research. |
| Kraken2 | /datasets/kraken2 | Kraken2 is used for fast taxonomic assignments of Metagenomic sequencing reads. Multiple collections are available: pluspfp, pracken, and standard. For details on running kraken2, please refer to our software page |