SPATA: A highly accurate GUI tool for de novo transcriptome assembly

Tin Chi Nguyen; Zhiyu Zhao; Dongxiao Zhu

doi:10.1109/BIBMW.2011.6112557

SPATA: A highly accurate GUI tool for de novo transcriptome assembly

Tin Chi Nguyen, Zhiyu Zhao, Dongxiao Zhu

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Abstract

RNA-seq reads are sampled from the underlying human transcriptome sequence, consisting of hundreds of thousands of mRNA transcripts. De novo transcriptome reconstruction from RNA-seq reads is a promising approach but facing with algorithmic and computational challenges derived from nonlinear transcript structures and ultra high-throughput read counts. To tackle this issue, we designed a divide-and-conquer strategy to read localization, followed by a novel algorithm to de novo read assembly. Availability: the GUI tool is freely available at http://asammate.sourceforge.net/.

Original language	English (US)
Title of host publication	2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011
Pages	1051-1053
Number of pages	3
DOIs	https://doi.org/10.1109/BIBMW.2011.6112557
State	Published - Dec 1 2011
Event	2011 IEEE International Conference onBioinformatics and Biomedicine Workshops, BIBMW 2011 - Atlanta, GA, United States Duration: Nov 12 2011 → Nov 15 2011

Publication series

Name	2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011

Other

Other	2011 IEEE International Conference onBioinformatics and Biomedicine Workshops, BIBMW 2011
Country/Territory	United States
City	Atlanta, GA
Period	11/12/11 → 11/15/11

Keywords

RNA-seq
de novo assembly
read mapping
transcriptome

ASJC Scopus subject areas

Biomedical Engineering
Health Informatics
Health Information Management

Access to Document

10.1109/BIBMW.2011.6112557

Cite this

Nguyen, T. C., Zhao, Z., & Zhu, D. (2011). SPATA: A highly accurate GUI tool for de novo transcriptome assembly. In 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011 (pp. 1051-1053). [6112557] (2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011). https://doi.org/10.1109/BIBMW.2011.6112557

SPATA: A highly accurate GUI tool for de novo transcriptome assembly. / Nguyen, Tin Chi; Zhao, Zhiyu; Zhu, Dongxiao.
2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011. 2011. p. 1051-1053 6112557 (2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Nguyen, TC, Zhao, Z & Zhu, D 2011, SPATA: A highly accurate GUI tool for de novo transcriptome assembly. in 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011., 6112557, 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011, pp. 1051-1053, 2011 IEEE International Conference onBioinformatics and Biomedicine Workshops, BIBMW 2011, Atlanta, GA, United States, 11/12/11. https://doi.org/10.1109/BIBMW.2011.6112557

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abstract = "RNA-seq reads are sampled from the underlying human transcriptome sequence, consisting of hundreds of thousands of mRNA transcripts. De novo transcriptome reconstruction from RNA-seq reads is a promising approach but facing with algorithmic and computational challenges derived from nonlinear transcript structures and ultra high-throughput read counts. To tackle this issue, we designed a divide-and-conquer strategy to read localization, followed by a novel algorithm to de novo read assembly. Availability: the GUI tool is freely available at http://asammate.sourceforge.net/.",

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SPATA: A highly accurate GUI tool for de novo transcriptome assembly

Abstract

Publication series

Other

Keywords

ASJC Scopus subject areas

Access to Document

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