Kraken
Supported Tool
is a taxonomic classification tool that uses exact k-mer matches to find the lowest common ancestor (LCA) of a given sequence.
Description
The MultiQC module supports outputs from both Kraken and Kraken 2.
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 FirmicutesA 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: 5File 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+)unclassified
num_lines: 1