Scientific Reference Data

We provide a set of centrally-maintained scientific reference databases for Biowulf users. You can search through this data here. To request a new database or an update, please contact us at staff@hpc.nih.gov.


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Browse Common Databases

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2024-04-13 taxonomy The Taxonomy Database is a curated classification and nomenclature for all of the organisms in the public sequence databases.
2024-04-02 TomoTwin Models Models for the particle picking software TomoTwin
2024-03-21 dorado models Models for the dorado basecaller by ONT
2024-03-15 Reference data for the cellranger pipeline References for the 10x Genomics cellranger pipeline
2024-03-13 VEP VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.
2024-03-03 dfam The Dfam database is a open collection of Transposable Element DNA sequence alignments, hidden Markov Models (HMMs), consensus sequences, and genome annotations.
2024-02-19 I-TASSER ITLIB I-TASSER Template Library for Protein Structure and Function Prediction
2024-02-03 Betacoronavirus Blast database of Betacoronavirus nucleotide sequences. (Blast database full path and name - /fdb/blastdb/Betacoronavirus)
2024-02-03 PDB protein sequences Blast db Protein Data Bank sequences. (Blast database full path and name - /fdb/blastdb/pdbaa )
2024-02-03 Swissprot Blast database Curated, highly-annotated protein sequence database (Blast database full path and name - /fdb/blastdb/swissprot )
2024-01-30 NCBI nt Blast database NCBI nonredundant comprehensive nucleotide database, compiled from Genbank, Refseq, TPA and PDB. (Blast database full path and name - /fdb/blastdb/nt )
2024-01-29 NCBI nr Blast database NCBI nonredundant comprehensive protein database, compiled from GenBank CDS translations, PDB, Swiss-Prot, PIR, and PRF (Blast database full path and name - /fdb/blastdb/nr )
2024-01-27 PDB nucleotide sequences Blast db Protein Data Bank nucleotide sequences. (Blast database full path and name - /fdb/blastdb/pdbnt )
2024-01-25 ensembl Ensembl is a genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation.
2024-01-21 colabfold sequence databases Databases used by colabfold for MSA generation with mmseqs2.
2024-01-16 Patent nucleotide sequences Blast db Patent nucleotide sequences (Blast database full path and name - /fdb/blastdb/patnt )
2024-01-12 VICTOR Reference Data Reference data for VICTOR application including GRCh37 and GRCh38. Also includes precomputed BayesDel meta-scores.
2023-12-20 Illumina iGenomes Ready-To-Use Reference Sequences and Annotations from Illumina for commonly analyzed organisms.
2023-12-11 gnomAD The Genome Aggregation Database (gnomAD) is a resource developed by an international coalition of investigators, with the goal of aggregating and harmonizing both exome and genome sequencing data from a wide variety of large-scale sequencing projects, and making summary data available for the wider scientific community.
2023-09-07 CheckM2 reference data Data used by CheckM2 to asses the quality of genome assemblies