Index a reference (possibly multiple references in a single fastx file) with FMD-index and save it to a file ("tai" Thermite Aligner Index file format)
Align reads from a fastx file by finding the longest single MEM shared between all the references and each read
Output in PAF format
Take a look at the README for running instructions.
Features:
tai" Thermite Aligner Index file format)Take a look at the README for running instructions.