Flowchart of customized workflow to detect and group invertons in hCom2 from metagenomic sequencing data. Briefly, PhaseFinderDC’s locate + create steps search the hCom2 reference genomes for inverted repeats (i.e., potential invertons) and create an augmented reference database including forward, reverse orientations for these repeats as well as intervening sequences. Shotgun metagenomic hCom2 short-read sequencing data is then mapped onto this database, and forward/reverse read counts are enumerated for each inverted repeat after MAPQ filtering for multi-mapping reads. Invertons are called if sufficient reverse/forward reads are detected, and then grouped by homology of their inverted repeat sequence.
