Setting -n to number of genomes, or number of genomes minus one? about pggb HOT 3 CLOSED

Hi @henrivkgt,

those -ns are not the same parameter. In the first example (https://pggb.readthedocs.io/en/latest/rst/tutorials/sequence_partitioning.html), -n refers to a parameter of wfmash (the sequence aligner we use in pggb). Instead, in the second example (https://pggb.readthedocs.io/en/latest/rst/quick_start.html), -n refers to a parameter of pggb.

Since they have the same name, I wonder if we should make the handling of these -ns the same from the outside (hiding the -1 thing) to avoid other confusion in the future.

from pggb.

Thank you, that makes sense.

from pggb.

This is a bad documentation bug. The tutorial isn't in sync with the code. pggb's help text also doesn't explain that this should be set equal to the number of expected homologous haplotypes within the pangenome.

The way to use -n is that it is equal to the number of haplotypes that you expect in your sample. For instance, if you had N=10 diploid genomes as input, you'd expect (typically) to see 2N=20 homologous copies of each locus. In this case, we should run pggb -n 20. If we just have 10 sequences, or 10 haploid genomes, we'd run pggb -n 10.

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