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