篇名 | A Re-sequencing Tool for Next Generation Sequencing Based on Burrows-wheeler Transform |
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卷期 | 21:4 |
作者 | Lu, Chen-hua 、 Lin, Chun-yuan 、 Tang, Chuan-yi |
頁次 | 037-052 |
關鍵字 | NGS 、 BWT 、 FM-index 、 re-sequencing 、 short read 、 DNA 、 EI 、 MEDLINE 、 Scopus |
出刊日期 | 201101 |
After the reference genomes of many organisms are sequenced in this post-genetic era, it has become 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. 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.