Sourmash

The module can summarise data from the following sourmash output files (descriptions from command line help output):

• sourmash compare
  • create a similarity matrix comparing many samples.
• sourmash gather
  • search a metagenome signature against databases.

Additional information on sourmash and its outputs is available on the sourmash documentation website.

sourmash gather is modelled after the Kraken module, and builds a bar graph that shows the coverage of top-5 genomes covered most by all samples. The number of top genomes can be customized in the config file:

sourmash:
  gather:
    top_n: 5

File search patterns

sourmash/compare:
  fn: "*.labels.txt"
sourmash/gather:
  contents: intersect_bp,f_orig_query,f_match,f_unique_to_query,f_unique_weighted,
  num_lines: 1