Demonstrating the utility of flexible sequence queries against indexed short reads with FlexTyper
Fig 2
Workflow for query search against the FM-index, starting with input queries and settings defined in Settings.ini file. In this figure, the example shows a centered search with ignoreNonUniqueKmers enabled. 1) K-mer generation has two modes centered search and sliding search. For a centered search, the position of interest lies in the middle of the query, and k-mers are designed to overlap that central position with defined length (k) and step (s). 2) If the ignore-duplicates option is set, k-mers collated from the query set are filtered to remove any k-mers which were found in multiple query sequences. 3) The filtered k-mers are then searched for within a single FM-index (left two panels) or multiple indexes (right two panels) of the read set. This can be done using single (top two panels) or multiple (bottom two panels) threads. 4) The results corresponding to a position within the FM-index are then translated back into reads, with hits on reverse complement reads assigned to the primary read, and collapsed into a set for each query. The final counts are reported per query.