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| Content Provider | World Health Organization (WHO)-Global Index Medicus |
|---|---|
| Author | Shih, Arthur Chun-chieh Liu, Tsunglin Lee, Greg C. Lu, Chen-hua Chu, Te-chin Li, Wen-hsiung |
| Description | Author Affiliation: Chu TC ( Institute of Information Science, Academia Sinica, Taipei 115, Taiwan.); |
| Abstract | Assembling a large genome using next generation sequencing reads requires large computer memory and a long execution time. To reduce these requirements, we propose an extension-based assembler, called JR-Assembler, where J and R stand for 'jumping' extension and read 'remapping.' First, it uses the read count to select good quality reads as seeds. Second, it extends each seed by a whole-read extension process, which expedites the extension process and can jump over short repeats. Third, it uses a dynamic back trimming process to avoid extension termination due to sequencing errors. Fourth, it remaps reads to each assembled sequence, and if an assembly error occurs by the presence of a repeat, it breaks the contig at the repeat boundaries. Fifth, it applies a less stringent extension criterion to connect low-coverage regions. Finally, it merges contigs by unused reads. An extensive comparison of JR-Assembler with current assemblers using datasets from small, medium, and large genomes shows that JR-Assembler achieves a better or comparable overall assembly quality and requires lower memory use and less central processing unit time, especially for large genomes. Finally, a simulation study shows that JR-Assembler achieves a superior performance on memory use and central processing unit time than most current assemblers when the read length is 150 bp or longer, indicating that the advantages of JR-Assembler over current assemblers will increase as the read length increases with advances in next generation sequencing technology. |
| ISSN | 00278424 |
| e-ISSN | 10916490 |
| Journal | Proceedings of the National Academy of Sciences of the United States of America |
| Issue Number | 36 |
| Volume Number | 110 |
| Language | English |
| Publisher | National Academy of Sciences |
| Publisher Date | 2013-09-01 |
| Publisher Place | United States |
| Access Restriction | Open |
| Subject Keyword | Computational Biology Genome, Bacterial Genome, Fungal High-Throughput Nucleotide Sequencing Instrumentation Statistics & Numerical Data Reproducibility Of Results Research Support, Non-U.S. Gov't Multidisciplinary |
| Content Type | Text |
| Resource Type | Article |
| Subject | Multidisciplinary |
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