NINJA-OPS: Fast Accurate Marker Gene Alignment Using Concatenated Ribosomes
NINJA core programs are represented by pentagons, data files by cylinders, processes within a program as lists, index operations as rounded rectangles, and other swappable programs by other shapes. The entire upper-left branch of the schematic (from input references to bowtie-build and TaxMap) does not need to be performed if using an existing database, such as that supplied with NINJA. The python wrapper encompasses the remaining two branches (bottom and right) for convenience. In general, Ninja_prep prepares the concatesome, Ninja_filter prepares the reads for alignment, bowtie2 (or any BWT-enabled aligner) performs the alignment, and Ninja_parse merges the various pieces into a complete OTU table.