Abstract
In this thesis, we present a re-sequencing tool designed for the Next Generation Sequencing (NGS) data. These data are composed huge amount of short reads, which are to align onto a referenced genome. We modified and implemented the algorithm of Borrows-Wheeler Transform and FM-index to build the genome index of human, and proposed an idea to segment each short read which lead us to align short reads with longer Hamming distance. Finally, we used 4 real data sets with different lengths form 1000 Genome Project to demonstrate the performance of our tool with a personal computer, and compared the results with a widely used tool, bowtie.