PGGB : PanGenome Graph Builder

Graph construction with PGGB §

Files preparation §

Note

Fasta must be mereged in a single file, for instance using cat *.fasta > out.fa. Then, it needs to be indexed with samtools faidx out.fa. Just specify the main out.fa file when using PGGB, it will find the indexed file by itself.

Build graph from multifasta files §

In the case you build from multiple individuals (files) with many entries (fasta fields), each . You will find reference to the files in the P-lines:

• the name given to the sample (cactus pipeline file) will be in the first field.
• the name of each fasta header will be in the third field.

PGGB output §

The pipeline outputs six different graphs, that corresponds to different steps of the pipeline.