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| Content Provider | PubMed Central |
|---|---|
| Author | Chu, Te-chin Lu, Chen-hua Liu, Tsunglin Lee, Greg C. Li, Wen-hsiung Shih, Arthur Chun-chieh |
| Abstract | Assembling a large genome faces three challenges: assembly quality, computer memory requirement, and execution time. Our developed assembler, JR-Assembler, uses (a) a strategy that selects good seeds for contig construction, (b) an extension strategy that uses whole sequencing reads to increase the chance to jump over repeats and to expedite extension, and (c) detecting misassemblies by remapping reads to assembled sequences. Compared with current assemblers, JR-Assembler achieves a better overall assembly quality, requires less execution time and requires, with one exception, less memory. The advantages of JR-Assembler in memory usage and execution time will increase slowly as the read length increases. Thus, contrary to the prevailing view, the extension approach seems superior to the de Bruijn graph approach. |
| Related Links | http://dx.doi.org/10.1073/pnas.1314090110 |
| Starting Page | 3417 |
| File Format | |
| 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 | 2013-09-03 |
| Access Restriction | Open |
| Rights Holder | National Academy of Sciences |
| Subject Keyword | General Research in Higher Education |
| Content Type | Text |
| Resource Type | Article |
| Subject | Multidisciplinary |
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