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 proceedingConference 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 languageEnglish (US)
Title of host publication2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011
Pages1051-1053
Number of pages3
DOIs
StatePublished - 2011
Event2011 IEEE International Conference onBioinformatics and Biomedicine Workshops, BIBMW 2011 - Atlanta, GA, United States
Duration: Nov 12 2011Nov 15 2011

Other

Other2011 IEEE International Conference onBioinformatics and Biomedicine Workshops, BIBMW 2011
CountryUnited States
CityAtlanta, GA
Period11/12/1111/15/11

Fingerprint

Graphical user interfaces
RNA
Transcriptome
Throughput
Availability
Messenger RNA

Keywords

  • de novo assembly
  • read mapping
  • RNA-seq
  • transcriptome

ASJC Scopus subject areas

  • Biomedical Engineering
  • Health Informatics
  • Health Information Management

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] 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.

Research output: Chapter in Book/Report/Conference proceedingConference 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, 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
Nguyen TC, Zhao Z, Zhu D. SPATA: A highly accurate GUI tool for de novo transcriptome assembly. In 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011. 2011. p. 1051-1053. 6112557 https://doi.org/10.1109/BIBMW.2011.6112557
Nguyen, Tin Chi ; Zhao, Zhiyu ; Zhu, Dongxiao. / SPATA : A highly accurate GUI tool for de novo transcriptome assembly. 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011. 2011. pp. 1051-1053
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