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Pangenome graph construction from genome alignments with Minigraph-Cactus.

Glenn Hickey¹, Jean Monlong², Jana Ebler^3,4

¹UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA. glenn.hickey@gmail.com.

Nature Biotechnology

|May 10, 2023

Summary

This study introduces the Minigraph-Cactus pipeline for building pangenome graphs directly from genome assemblies. This approach improves genetic variation representation and analysis accuracy, especially with high-quality references like CHM13.

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Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Reference genomes present biases due to limited haplotype representation.
Pangenome references, often graph-based, store diverse haplotypes to mitigate these biases.
Advances in long-read sequencing yield high-quality phased assemblies, enabling new pangenome construction methods.

Purpose of the Study:

To present the Minigraph-Cactus pipeline for constructing pangenome graphs directly from whole-genome alignments.
To demonstrate the scalability of the pipeline using 90 human haplotypes.
To evaluate the impact of reference genome quality on pangenome construction and downstream analyses.

Main Methods:

Developed the Minigraph-Cactus pipeline to generate pangenomes from whole-genome alignments.
Applied the pipeline to 90 haplotypes from the Human Pangenome Reference Consortium.
Integrated the CHM13 human reference genome into the pangenome construction process.
Constructed a pangenome for Drosophila melanogaster.

Main Results:

The Minigraph-Cactus pipeline successfully scaled to 90 human haplotypes.
Pangenome graphs built directly from assemblies capture diverse genetic variations at multiple scales.
Utilizing the CHM13 reference significantly improved the accuracy of the pangenome analysis.
Demonstrated successful pangenome construction for Drosophila melanogaster.

Conclusions:

Direct construction of pangenome graphs from assemblies offers a robust method for representing genetic variation.
The Minigraph-Cactus pipeline provides a scalable and accurate tool for pangenome construction.
High-quality, complete reference genomes are crucial for enhancing the accuracy of pangenome-based genomic analyses.