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pangenome / pggb

the pangenome graph builder
https://doi.org/10.1038/s41592-024-02430-3
MIT License
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Skip sequence partitioning? #278

Closed fangbohao closed 2 days ago

fangbohao commented 1 year ago

Hi, I was wondering if I could just skip the sequence partitioning because there is a chromosome-level genome provided by the VGP project. Could I just subset chromosomes based on the VGP reference genome for my HiFi haplotype contigs? Is there any hidden issue if I skip this step?

Thanks! Bohao

AndreaGuarracino commented 1 year ago

Hi @fangbohao, you can skip the partitioning, it is not a mandatory step. We recommend creating subsets of contigs, when possible and if it makes sense for the specific analysis, to reduce the computational work for PGGB.

fangbohao commented 1 year ago

Thanks for your comments, Andrea!