Process graph

Graph processing

vg stats

Reports graph statistics.

Usage: vg stats [options] [<graph file>]

Example grave command:

vg stats --threads ${task.cpus} -zlLHTA ${graph}

• z size of the graph
• l length of sequences in the graph
• L number of self loops
• H list the head nodes of the graph
• T list the tail nodes of the graph
• A report if the graph is acyclic or not

vg paths

Reports path metadata from the graph.

Usage: vg paths [options]

Example grave command:

vg paths --metadata -x ${graph} > ${basename}_graph-metadata.txt

vg paths (2)

Extract reference FASTA from the graph.

Example grave command:

vg paths --reference-paths --extract-fasta -x ${graph} > reference.fasta