HPRC Tutorials

The Human Pangenome Reference Consortium produces and releases to the public sequencing data, assemblies, and pangenomes. This repository houses tutorials for accessing and using HPRC tools and data.

For information about data reuse and publicating with HPRC data please see the HPRC's Data Use Protocol. If you would like to publish using this please contact the HPRC Coordinating Center at [email protected].

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HPRC Pangenome Workshop at the Human Genome Meeting (Rome 2024)

This workshop took place in Rome on April, 8 2024 for Human Genome Meeting (HUGO). After some introductions around the project and pangenomes, the participants first built and analyzed pangenomes with PGGB. In the second part, Giraffe was used to map short sequencing reads to a slice of the HPRC pangenome and small variants were called using DeepVariant.

The materials for the workshop are available under pangenome/240408_HumanGenomeMeeting_HUGO.

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Short Read Variant Calling With Giraffe & DeepVariant

This tutorial demonstrates variant calling using the Human Pangenome Reference Consortium's (HPRC) year 1 Minigraph/CACTUS pangenome with the Giraffe/DeepVariant pipeline for calling germline small variants. This workspace is intended to be a demonstration of utilizing a pangenome from the HPRC in AnVIL and Terra.

Instructions and a brief overview of the process can be found under pangenome/giraffe-deepvariant.