Organism Example Parameters

Human

The following parameters were used to build a 90-haplotype human pangenome graph from the HPRC data. Specifically, the graph built contains the human references GRCh38, CHM13, and the contigs of 44 diploid individuals that encode all possible variations including those in telomeres and centromeres.

pggb -p 98 -s 50000 -n 90 -k 79 ...

Major Histocompatibility Complex

We built a pangenome graph from 9 MHC class II assemblies from vertebrate genomes which have 5-10% divergence.

pggb -n 9 -k 29 ...

Helicobacter

Building a pangenome graph from 15 helicobacter genomes with 5% divergence.

pggb -n 15 -k 79 ...

Building a pangenome graph from 15 helicobacter genomes with 10% divergence.

pggb -n 15 -k 19 -P asm20 ...

Yeast

Building a pangenome graph from 7 yeast genomes with 5% divergence.

pggb -n 7 -k 29 ...

Bacterial genomes

Building a pangenome graph from A few thousand bacterial genomes.

pggb -x auto -n 2146 ...

In general mapping sparsification (-x auto) is a good idea when you have many hundreds to thousands of genomes.