Pangenome Resources and Graph Creation Strategies
Pangenome Resources provide insights into Pangenomic data formats like GFA and rGFA, with tools such as Minigraph, Minigraph-CACTUS, and PGGB. Explore Graph Creation Strategies with different data sizes and node numbers for effective pangenome analysis, scaling, and optimization.
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https://humanpangenome.org/data/ https://github.com/human-pangenomics/hpp_pangenome_resources HPRC PANGENOME RESOURCES
HPRC Pangenome Resources Pangenomic data formats GFA (The Graphical Fragment Assembly) Segment: a continuous sequence or subsequence. Link: an overlap between two segments. Each link is from the end of one segment to the beginning of another segment. The link stores the orientation of each segment and the amount of basepairs overlapping. Containment: an overlap between two segments where one is contained in the other. Path: an ordered list of oriented segments, where each consecutive pair of oriented segments is supported by a link or a jump record. 3/6/2025 2
HPRC Pangenome Resources Pangenomic data formats GFA (The Graphical Fragment Assembly) 3/6/2025 3
HPRC Pangenome Resources Pangenomic data formats rGFA(The Reference GFA) rGFA is a strict subset of GFA. It disallows overlaps between segments and requires three additional tags on each segment. 3/6/2025 4
HPRC Pangenome Resources HPRC Human Pangenome Reference Consortium Currently there are three main approaches: Minigraph Minigraph-CACTUS Pangenome Graph Builder (PGGB) Each pangenome has different strengths and weaknesses. 3/6/2025 5
HPRC Pangenome Resources Graph Creation Strategies 3/6/2025 6
HPRC Pangenome Resources Graph Creation Strategies Strategies data formats data size number of the nodes Minigraph rGAF 3.2GB about 425K Minigraph-Cactus GAF 47.1GB over 80M PGGB GAF 92.8GB over 110M 3/6/2025 7
HPRC Pangenome Resources Disscuss The scale of the number of nodes Minigraph Part of PGGB Without genome annotation Genome annotation dataset Offset PanTools Pangenome to KG 3/6/2025 8
HPRC Pangenome Resources Thanks! 3/6/2025 9
