Pepkio Cloud
Public reference datasets
We curate commonly used public reference data across genomics, transcriptomics, proteomics, metabolomics, and microbiome. Browse the names below. During analysis, agents use Cloud Skills to pick versions and download locations.
Now working with early users.
How to use
Researchers: scan the name lists below to confirm coverage for your species and omics.
Agents: after connecting Cloud MCP, read references/datasets/ in the pepkio-cloud skill for versions and download guidance.
Shared references by species
Human
- GENCODE v50 human primary assembly genome (GRCh38)
- GENCODE v50 human gene annotation (GTF)
- GENCODE v50 human transcript sequences
- NCBI RefSeq GRCh38 annotation
- T2T-CHM13v2 genome
- Ensembl human GRCh38 primary assembly
- GENCODE GRCh37 / hg19 legacy reference
- GENCODE v50 human release README
- GENCODE v50 human gene ID mapping tables
- HGNC human gene symbols
- Broad GATK hg38 reference bundle
- Broad GATK hg19 / b37 reference bundle
- gnomAD v4.1 population variants
- dbSNP latest GRCh38 VCF
- GENCODE v50 human lncRNA transcripts
- 10x Cell Ranger GRCh38 2024-A reference
- 10x Cell Ranger GRCh38 and GRCm39 2024-A mixed reference
- 10x Cell Ranger human V(D)J reference
- UniProt human proteome (UP000005640)
- HMDB metabolite structures
Mouse
- GENCODE M39 mouse primary assembly genome (GRCm39)
- GENCODE M39 mouse gene annotation (GTF)
- GENCODE M39 mouse transcript sequences
- NCBI RefSeq GRCm39 annotation
- Ensembl mouse GRCm39 primary assembly
- GENCODE M39 mouse release README
- GENCODE M39 mouse gene ID mapping tables
- MGI mouse gene symbols
- 10x Cell Ranger GRCm39 2024-A reference
- 10x Cell Ranger GRCh38 and GRCm39 2024-A mixed reference
- UniProt mouse proteome (UP000000589)
Other model organisms
- Ensembl rat mRatBN7.2 reference
- Ensembl zebrafish GRCz11 reference
- Ensembl fruit fly BDGP6 reference
- Arabidopsis TAIR10 / Araport11 reference
By omics
Genomics
- GENCODE v50 human primary assembly genome (GRCh38)
- GENCODE v50 human gene annotation (GTF)
- NCBI RefSeq GRCh38 annotation
- T2T-CHM13v2 genome
- Ensembl human GRCh38 primary assembly
- GENCODE M39 mouse primary assembly genome (GRCm39)
- GENCODE M39 mouse gene annotation (GTF)
- NCBI RefSeq GRCm39 annotation
- Ensembl mouse GRCm39 primary assembly
- Broad GATK hg38 reference bundle
- Broad GATK hg19 / b37 reference bundle
- gnomAD v4.1 population variants
- dbSNP latest GRCh38 VCF
Transcriptomics
- GENCODE v50 human primary assembly genome (GRCh38)
- GENCODE v50 human gene annotation (GTF)
- GENCODE v50 human transcript sequences
- NCBI RefSeq GRCh38 annotation
- Ensembl human GRCh38 primary assembly
- GENCODE M39 mouse primary assembly genome (GRCm39)
- GENCODE M39 mouse gene annotation (GTF)
- GENCODE M39 mouse transcript sequences
- NCBI RefSeq GRCm39 annotation
- Ensembl mouse GRCm39 primary assembly
- GENCODE v50 human lncRNA transcripts
- 10x Cell Ranger GRCh38 2024-A reference
- 10x Cell Ranger GRCm39 2024-A reference
- 10x Cell Ranger GRCh38 and GRCm39 2024-A mixed reference
- 10x Cell Ranger human V(D)J reference
- SILVA 138.2 SSU Ref NR 99
Proteomics
- UniProtKB Swiss-Prot protein sequences
- UniProtKB Swiss-Prot isoforms
- UniProt human proteome (UP000005640)
- UniProt mouse proteome (UP000000589)
- cRAP common contaminant proteins
Metabolomics
- HMDB metabolite structures
- ChEBI chemical ontology
- MassBank spectral library
- GNPS public spectral libraries
- LIPID MAPS LMSD
Microbiome
- SILVA 138.2 SSU Ref NR 99
- SILVA 138.2 LSU Ref NR 99
- GTDB latest genome taxonomy
- Kraken2 viral prebuilt index
FAQ
- What kinds of data are listed?
- Names are grouped by species (human, mouse, and other model organisms) and by omics (genomics, transcriptomics, proteomics, metabolomics, microbiome).
- How does an agent get the files?
- Connect Cloud MCP and read references/datasets/ in the pepkio-cloud (laptop) or pepkio-cloud-remote (workspace) skill. Skills carry version rules and download guidance — this page lists names only.
- Will the list grow?
- Yes. Early Access continues to expand the catalog. Feedback on missing references is welcome.
- What about the platform-mounted hg38 copies?
- Pepkio Cloud can mount a small set of shared references read-only at /datasets on a running cloud server. The names below are the broader curated catalog agents use to find official sources.