De novo assembly and analysis of RNA-seq data
We describe Trans-ABySS, a de novo short-read transcriptome assembly and analysis pipeline that addresses variation in local read densities by assembling read substrings with varying stringencies and then merging the resulting contigs before analysis. Analyzing 7.4 gigabases of 50-base-pair paired-e...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Journal Article |
| Published: |
2010
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| Online Access: | http://hdl.handle.net/20.500.11937/16548 |
| _version_ | 1848749207914020864 |
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| author | Robertson, G. Schein, J. Chiu, R. Corbett, R. Field, M. Jackman, S. Mungall, K. Lee, S. Okada, H. Qian, J. Griffith, M. Raymond, A. Thiessen, N. Cezard, T. Butterfield, Y. Newsome, R. Chan, S. She, R. Varhol, Richard Kamoh, B. Prabhu, A. Tam, A. Zhao, Y. Moore, R. Hirst, M. Marra, M. Jones, S. Hoodless, P. Birol, I. |
| author_facet | Robertson, G. Schein, J. Chiu, R. Corbett, R. Field, M. Jackman, S. Mungall, K. Lee, S. Okada, H. Qian, J. Griffith, M. Raymond, A. Thiessen, N. Cezard, T. Butterfield, Y. Newsome, R. Chan, S. She, R. Varhol, Richard Kamoh, B. Prabhu, A. Tam, A. Zhao, Y. Moore, R. Hirst, M. Marra, M. Jones, S. Hoodless, P. Birol, I. |
| author_sort | Robertson, G. |
| building | Curtin Institutional Repository |
| collection | Online Access |
| description | We describe Trans-ABySS, a de novo short-read transcriptome assembly and analysis pipeline that addresses variation in local read densities by assembling read substrings with varying stringencies and then merging the resulting contigs before analysis. Analyzing 7.4 gigabases of 50-base-pair paired-end Illumina reads from an adult mouse liver poly(A) RNA library, we identified known, new and alternative structures in expressed transcripts, and achieved high sensitivity and specificity relative to reference-based assembly methods. © 2010 Nature America, Inc. All rights reserved. |
| first_indexed | 2025-11-14T07:17:16Z |
| format | Journal Article |
| id | curtin-20.500.11937-16548 |
| institution | Curtin University Malaysia |
| institution_category | Local University |
| last_indexed | 2025-11-14T07:17:16Z |
| publishDate | 2010 |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | curtin-20.500.11937-165482017-09-13T15:43:55Z De novo assembly and analysis of RNA-seq data Robertson, G. Schein, J. Chiu, R. Corbett, R. Field, M. Jackman, S. Mungall, K. Lee, S. Okada, H. Qian, J. Griffith, M. Raymond, A. Thiessen, N. Cezard, T. Butterfield, Y. Newsome, R. Chan, S. She, R. Varhol, Richard Kamoh, B. Prabhu, A. Tam, A. Zhao, Y. Moore, R. Hirst, M. Marra, M. Jones, S. Hoodless, P. Birol, I. We describe Trans-ABySS, a de novo short-read transcriptome assembly and analysis pipeline that addresses variation in local read densities by assembling read substrings with varying stringencies and then merging the resulting contigs before analysis. Analyzing 7.4 gigabases of 50-base-pair paired-end Illumina reads from an adult mouse liver poly(A) RNA library, we identified known, new and alternative structures in expressed transcripts, and achieved high sensitivity and specificity relative to reference-based assembly methods. © 2010 Nature America, Inc. All rights reserved. 2010 Journal Article http://hdl.handle.net/20.500.11937/16548 10.1038/nmeth.1517 restricted |
| spellingShingle | Robertson, G. Schein, J. Chiu, R. Corbett, R. Field, M. Jackman, S. Mungall, K. Lee, S. Okada, H. Qian, J. Griffith, M. Raymond, A. Thiessen, N. Cezard, T. Butterfield, Y. Newsome, R. Chan, S. She, R. Varhol, Richard Kamoh, B. Prabhu, A. Tam, A. Zhao, Y. Moore, R. Hirst, M. Marra, M. Jones, S. Hoodless, P. Birol, I. De novo assembly and analysis of RNA-seq data |
| title | De novo assembly and analysis of RNA-seq data |
| title_full | De novo assembly and analysis of RNA-seq data |
| title_fullStr | De novo assembly and analysis of RNA-seq data |
| title_full_unstemmed | De novo assembly and analysis of RNA-seq data |
| title_short | De novo assembly and analysis of RNA-seq data |
| title_sort | de novo assembly and analysis of rna-seq data |
| url | http://hdl.handle.net/20.500.11937/16548 |