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Kraken

note

Taxonomic classification using exact k-mer matches to find the lowest common ancestor (LCA) of a given sequence.

https://ccb.jhu.edu/software/kraken/

The MultiQC module supports outputs from Kraken.

It works with report files generated using the --report flag, that look like the following:

11.66	98148	98148	U	0	unclassified
88.34	743870	996	-	1	root
88.22	742867	0	-	131567	  cellular organisms
88.22	742866	2071	D	2	    Bacteria
87.95	740514	2914	P	1239	      Firmicutes

A bar graph is generated that shows the number of fragments for each sample that fall into the top-5 categories for each taxa rank. The top categories are calculated by summing the library percentages across all samples.

The number of top categories to plot can be customized in the config file:

kraken:
  top_n: 5

The module also handles Bracken outputs, which uses Kraken internally.

File search patterns​

kraken:
  contents_re: ^\s{0,2}(\d{1,3}\.\d{1,2})\t(\d+)\t(\d+)\t((\d+)\t(\d+)\t)?([URDKPCOFGS-]\d{0,2})\t(\d+)(\s+)[root|unclassified]
  num_lines: 2