De novo transcriptome assembly with ABySS
Motivation: Whole transcriptome shotgun sequencing data from non-normalized samples offer unique opportunities to study the metabolic states of organisms. One can deduce gene expression levels using sequence coverage as a surrogate, identify coding changes or discover novel isoforms or transcripts....
| Main Authors: | , , , , , , , , , , , , , , |
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| Format: | Journal Article |
| Published: |
Oxford University Press
2009
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| Online Access: | http://hdl.handle.net/20.500.11937/46618 |
| _version_ | 1848757609401679872 |
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| author | Birol, I. Jackman, S. Nielsen, C. Qian, J. Varhol, Richard Stazyk, G. Morin, R. Zhao, Y. Hirst, M. Schein, J. Horsman, D. Connors, J. Gascoyne, R. Marra, M. Jones, S. |
| author_facet | Birol, I. Jackman, S. Nielsen, C. Qian, J. Varhol, Richard Stazyk, G. Morin, R. Zhao, Y. Hirst, M. Schein, J. Horsman, D. Connors, J. Gascoyne, R. Marra, M. Jones, S. |
| author_sort | Birol, I. |
| building | Curtin Institutional Repository |
| collection | Online Access |
| description | Motivation: Whole transcriptome shotgun sequencing data from non-normalized samples offer unique opportunities to study the metabolic states of organisms. One can deduce gene expression levels using sequence coverage as a surrogate, identify coding changes or discover novel isoforms or transcripts. Especially for discovery of novel events, de novo assembly of transcriptomes is desirable. Results: Transcriptome from tumor tissue of a patient with follicular lymphoma was sequenced with 36 base pair (bp) single- and paired-end reads on the Illumina Genome Analyzer II platform. We assembled ~194 million reads using ABySS into 66 921 contigs 100 bp or longer, with a maximum contig length of 10 951 bp, representing over 30 million base pairs of unique transcriptome sequence, or roughly 1% of the genome. © The Author 2009. Published by Oxford University Press. All rights reserved. |
| first_indexed | 2025-11-14T09:30:49Z |
| format | Journal Article |
| id | curtin-20.500.11937-46618 |
| institution | Curtin University Malaysia |
| institution_category | Local University |
| last_indexed | 2025-11-14T09:30:49Z |
| publishDate | 2009 |
| publisher | Oxford University Press |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | curtin-20.500.11937-466182017-09-13T14:08:02Z De novo transcriptome assembly with ABySS Birol, I. Jackman, S. Nielsen, C. Qian, J. Varhol, Richard Stazyk, G. Morin, R. Zhao, Y. Hirst, M. Schein, J. Horsman, D. Connors, J. Gascoyne, R. Marra, M. Jones, S. Motivation: Whole transcriptome shotgun sequencing data from non-normalized samples offer unique opportunities to study the metabolic states of organisms. One can deduce gene expression levels using sequence coverage as a surrogate, identify coding changes or discover novel isoforms or transcripts. Especially for discovery of novel events, de novo assembly of transcriptomes is desirable. Results: Transcriptome from tumor tissue of a patient with follicular lymphoma was sequenced with 36 base pair (bp) single- and paired-end reads on the Illumina Genome Analyzer II platform. We assembled ~194 million reads using ABySS into 66 921 contigs 100 bp or longer, with a maximum contig length of 10 951 bp, representing over 30 million base pairs of unique transcriptome sequence, or roughly 1% of the genome. © The Author 2009. Published by Oxford University Press. All rights reserved. 2009 Journal Article http://hdl.handle.net/20.500.11937/46618 10.1093/bioinformatics/btp367 Oxford University Press unknown |
| spellingShingle | Birol, I. Jackman, S. Nielsen, C. Qian, J. Varhol, Richard Stazyk, G. Morin, R. Zhao, Y. Hirst, M. Schein, J. Horsman, D. Connors, J. Gascoyne, R. Marra, M. Jones, S. De novo transcriptome assembly with ABySS |
| title | De novo transcriptome assembly with ABySS |
| title_full | De novo transcriptome assembly with ABySS |
| title_fullStr | De novo transcriptome assembly with ABySS |
| title_full_unstemmed | De novo transcriptome assembly with ABySS |
| title_short | De novo transcriptome assembly with ABySS |
| title_sort | de novo transcriptome assembly with abyss |
| url | http://hdl.handle.net/20.500.11937/46618 |