A Re-sequencing Tool for Next Generation Sequencing based on Burrows-wheeler Transform Chen Hua Lu 1 , Chun Yuan Lin 2,＊ , and Chuan Yi Tang 3 1 Department of Computer Science, National Tsing Hua University, Hsinchu 300, Taiwan, ROC walterlu21@yahoo.com.tw 2 Department of Computer Science and Information Engineering, Chang Gung University, Taoyuan 330, Taiwan, ROC cyulin@mail.cgu.edu.tw 3 Department of Computer Science and Information Engineering, Providence University, Taichung 433, Taiwan, ROC cytang@pu.edu.tw Received 5 October 2010; Revised 15 November 2010; Accepted 10 December 2010 Abstract. After the reference genomes of many organisms are sequenced in this post-genetic era, it has be- come an extremely important issue that how to do the re-sequencing and assembly for individual genomes from very large amount of reads. In this paper, we will present a re-sequencing tool designed for the Next Generation Sequencing (NGS) data. And these data are composed of a huge amount of short reads which will be aligned onto a reference genome. We modified and implemented the algorithm of Burrows-Wheeler Transform and FM-index to build the genome index of human, and proposed an idea to segment each short read into multiple non-overlapping seeds, which let us align short reads with large Hamming distance. Fi- nally, we used 4 real data sets with different lengths form 1000 Genome Project to demonstrate the perform- ance of our tool with a personal computer, and compared the results with a widely used tool, bowtie. Keywords: NGS, BWT, FM-index, re-sequencing, short read, DNA References [1] P. Flicek and E. Birney, “Sense from Sequence Reads: Methods for Alignment and Assembly,” Nature Methods, Vol. 6, pp. 6-12, 2009. [2] H. Li, J. Ruan, R. Durbin, “Mapping Short DNA Sequencing Reads and Calling Variants Using Mapping Quality Scores,” Genome Research, Vol. 18, No. 11, pp. 1851-1858, 2008. [3] R. Li, Y. Li, K. Kristiansen, J. Wang, “SOAP: Short Oligonucleotide Alignment Program,” Bioinformatics, Vol. 24, No. 5, pp. 713-714, 2008. [4] D. Smith, Z. Xuan, M.Q. Zhang, “Using Quality Scores and Longer Reads Improves Accuracy of Solexa Read Map- ping,” BMC Bioinformatics, Vol. 9, No. 128, 2008. [5] H. Jiang and W.H. Wong, “SeqMap: Mapping Massive Amount of Oligonucleotides to the Genome,” Bioinformatics, Vol. 24, No. 20, pp. 2395-2396, 2008. [6] B. Langmead, C. Trapnell, M. Pop, S. L. Salzberg, “Ultrafast and Memory-efficient Alignment of Short DNA Se- quences to The Human Genome,” Genome Biology, Vol. 10, No. 3, pp. R25.1-R25.10, 2009. ＊ Correspondence author