The Full-text index in Minute space (FM-index) derived from the Burrows-Wheeler transform (BWT) is broadly used for fast string matching in large genomes or a huge set of sequencing reads. Several graphic processing unit (GPU) accelerated aligners based on the FM-index have been proposed recently, however, the construction of the index is still handled by central processing unit (CPU), only parallelized in data level (e.g. by performing blockwise suffix sorting in GPU), or not scalable for large genomes.