Fig. 1

Overview of the ConClave sorting scheme applied to species identification in metagenomic data sets. The figure represents a data set containing 5 sequence reads (4 bp) and two closely related reference sequences (templates), including a true positive (Ref. 1) and a potential false positive (Ref. 2). a Commonly used read mappers yield a high number of false positives because reads can be randomly assigned to closely related reference sequences sharing identical fragments spanning the whole sequence read (represented by the ATATT region). b The KMA aligner minimizes this problem by scoring reference sequences based on all possible mappings of all reads and then choosing the templates with the highest scores. Coupled with KMA, CCMetagen produces highly accurate taxonomic assignments of reads in metagenomic data sets in user-friendly formats