Skip to main content

odgi

The odgi module parses odgi stats reports. It is specifically designed to parse the output of

odgi stats -i input_graph.og -y

It is not guaranteed that output created using any other parameter combination can be parsed using this module. It solely works with report files generated by odgi stats in .yaml format, which look like the following:

---
length: 206263
nodes: 3751
edges: 5195
paths: 13
num_weakly_connected_components: 1
weakly_connected_components:
  - component:
      id: 0
      nodes: 3751
      is_acyclic: "no"
num_nodes_self_loops:
  total: 0
  unique: 0
A: 57554
C: 43275
G: 41944
T: 63490
mean_links_length:
  - length:
      path: all_paths
      in_node_space: 1.64973
      in_nucleotide_space: 7.34035
      num_links_considered: 202793
      num_gap_links_not_penalized: 147940
sum_of_path_node_distances:
  - distance:
    path: all_paths
    in_node_space: 5.53383
    in_nucleotide_space: 2.1454
    nodes: 202806
    nucleotides: 3757597
    num_penalties: 231
    num_penalties_different_orientation: 0

For the odgi module to discover the odgi stats reports, the file must match one of the following patterns:

  • "*.og.stats.yaml"
  • "*.og.stats.yml"
  • "*.odgi.stats.yaml"
  • "*.odgi.stats.yml"

A bar graph is generated, which shows the length, number of nodes, edges and paths for each sample. Additionally, a second bar graph is generated visualizing the in_node_space and in_nucleotide_space for every sample.

It is possible to add custom content to your MultiQC report including odgi viz or odgi draw PNGs. Ensure that the names of the PNGs match *_odgi_viz_mqc.png.