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| Content Provider | IEEE Xplore Digital Library |
|---|---|
| Author | Chen Hua Lu Chun Yuan Lin Chuan Yi Tang |
| Copyright Year | 2010 |
| Description | Author affiliation: Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan (Chen Hua Lu; Chuan Yi Tang) || Department of Computer Science and Information Engineering, Chang Gung University, Tao-Yuan, Taiwan (Chun Yuan Lin) |
| Abstract | 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 the simulated datasets and real datasets from 1000 Genome Project to demonstrate the performance of our tool on a personal computer, and compared the results with widely used tools, bowtie and SOAPv2. |
| Starting Page | 549 |
| Ending Page | 554 |
| File Size | 391422 |
| Page Count | 6 |
| File Format | |
| ISBN | 9781424483037 |
| e-ISBN | 9781424483044 |
| DOI | 10.1109/BIBMW.2010.5703860 |
| Language | English |
| Publisher | Institute of Electrical and Electronics Engineers, Inc. (IEEE) |
| Publisher Date | 2010-12-18 |
| Publisher Place | China |
| Access Restriction | Subscribed |
| Rights Holder | Institute of Electrical and Electronics Engineers, Inc. (IEEE) |
| Subject Keyword | Resequence Alignment Hamming distance Memory management Genomics Short Reads NGS Arrays Pattern matching BWT Indexing |
| Content Type | Text |
| Resource Type | Article |
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