Data
The Human Pangenome Reference Consortium generates raw sequencing data, high-quality assemblies, and pangenomes. All data generated is open, publicly accessible, and can be downloaded or used in AWS, GCP, AnVIL, or locally.
Data Availability
Sequencing data, assemblies, and pangenomes are stored in publicly accesible cloud buckets, the AnVIL data ecosystem, and in SRA/ENA/DDBJ.
- Data is uploaded to both AWS S3 and Google Cloud buckets. GitHub repositories have been created and include details about the data generation as well as index files with locations of the data stored in S3 and GCP. The HPRC S3 bucket does not charge egress fees making it a good option if you would like to download data to your local machine.
- AnVIL is a cloud environment that allows you to view the data organized in convenient data tables that refer to copies of the data in GCP. AnVIL also includes a workflow runner so you can analyze the data withough.
- All data is also uploaded to INSDCs (SRA/ENA/DDBJ) in BioProjects for sequencing data, assemblies, and pangenomes.
Sequencing Data Release2
- PacBio HiFi (with modification calls)
- PacBio Kinex
- Oxford Nanopore Ultralong (with modification calls)
- Omni-C/Hi-C
In addition, we include high coverage Illumina data produced by the NYGC for parents and children (when available). If you would like to download the files, data indexes are available in the GitHub repository.
Assemblies Release2
Assemblies produced with Hifiasm are available alongside annotations for the assemblies. If you would like to download the files, data indexes are available in the GitHub repository.
Pangenomes Release1
The HPRC has released pangenomes from its year 1 data. Currently there are three main approaches:
- Minigraph
- Minigraph-CACTUS
- Pangenome Graph Builder (PGGB)
Each pangenome has different strengths and weaknessness. If you do not know which pangenome best suits your needs, see the GitHub repository.
