Recentrifuge: Robust comparative analysis and contamination removal for metagenomics
Fig 1
Operating with taxonomic trees.
(A) Example of the recursive function which ‘folds the tree’ to prepare the taxonomic trees for further operations, with the parameter mintaxa set to 10 (explicitly for this example), and the minimum rank of interest minrank set to ‘genus.’ Initially, their trees show the direct taxonomic classification results. Then, recursively, the leaves of the tree are accumulated in the parent node if their number of assigned reads is under mintaxa (shown in red and bold counts) or if their corresponding taxonomic rank is below minrank. In this ‘folding’ the parent score is updated with a weighted average of its own score and the ones of the descendants that are being accumulated. E.g., after the 1st step, the G1 taxon at the sample is updated with np = 2 + 4 + 2 = 8 counts and score of . As the counts for G1 are still under mintaxa, in the 2nd step they are accumulated in F1 and its score updated to
. (B) Continuing with the example in (A), at genus level, there are two derived samples: the right one with the control removed from Sample1, the left one with the exclusive taxa of Sample2 (those taxa not present in the rest of samples, in this case, the control and Sample1).