SPATA: A seeding and patching algorithm for de novo transcriptome assembly

Zhiyu Zhao, Tin Chi Nguyen, Nan Deng, Kristen Marie Johnson, Dongxiao Zhu

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2 Scopus citations

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 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 perform reads localization followed by a novel algorithm to assemble reads de novo. Using simulation studies, we have demonstrated a high accuracy in transcriptome structures reconstruction.

Original languageEnglish (US)
Title of host publication2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011
Pages26-33
Number of pages8
DOIs
StatePublished - Dec 1 2011
Event2011 IEEE International Conference onBioinformatics and Biomedicine Workshops, BIBMW 2011 - Atlanta, GA, United States
Duration: Nov 12 2011Nov 15 2011

Publication series

Name2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011

Other

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

Keywords

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

ASJC Scopus subject areas

  • Biomedical Engineering
  • Health Informatics
  • Health Information Management

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