Analysis of transcriptome assembly pipelines for wheat

Natasha Pavlovikj, Kevin Begcy, Sairam Behera, Malachy Campbell, Harkamal Walia, Jitender S. Deogun

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

Abstract

With advances in next-generation sequencing technologies, transcriptome sequencing has emerged as a powerful tool for performing transcriptome analysis for various organisms. Obtaining draft transcriptome of an organism is a complex multi-stage pipeline with several steps such as data cleaning, error correction and assembly. Based on the analysis performed in this paper, we conclude that the best assembly is produced when the error correction method is used with Velvet Oases and the 'multi-k' strategy that combines the 5 k-mer assemblies with highest N50. Our results provide valuable insight for designing good de novo transcriptome assembly pipeline for a given application.

Original languageEnglish (US)
Title of host publicationProceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016
EditorsKevin Burrage, Qian Zhu, Yunlong Liu, Tianhai Tian, Yadong Wang, Xiaohua Tony Hu, Qinghua Jiang, Jiangning Song, Shinichi Morishita, Kevin Burrage, Guohua Wang
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages137-140
Number of pages4
ISBN (Electronic)9781509016105
DOIs
StatePublished - Jan 17 2017
Event2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016 - Shenzhen, China
Duration: Dec 15 2016Dec 18 2016

Publication series

NameProceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016

Other

Other2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016
CountryChina
CityShenzhen
Period12/15/1612/18/16

Fingerprint

Gene Expression Profiling
Transcriptome
Triticum
Pipelines
Error correction
Technology
Cleaning

Keywords

  • De novo assembly
  • Digital normalization
  • Error correction
  • K-mer length
  • Multi-k method
  • Transcriptome assembly

ASJC Scopus subject areas

  • Genetics
  • Medicine (miscellaneous)
  • Genetics(clinical)
  • Biochemistry, medical
  • Biochemistry
  • Molecular Medicine
  • Health Informatics

Cite this

Pavlovikj, N., Begcy, K., Behera, S., Campbell, M., Walia, H., & Deogun, J. S. (2017). Analysis of transcriptome assembly pipelines for wheat. In K. Burrage, Q. Zhu, Y. Liu, T. Tian, Y. Wang, X. T. Hu, Q. Jiang, J. Song, S. Morishita, K. Burrage, ... G. Wang (Eds.), Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016 (pp. 137-140). [7822507] (Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/BIBM.2016.7822507

Analysis of transcriptome assembly pipelines for wheat. / Pavlovikj, Natasha; Begcy, Kevin; Behera, Sairam; Campbell, Malachy; Walia, Harkamal; Deogun, Jitender S.

Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016. ed. / Kevin Burrage; Qian Zhu; Yunlong Liu; Tianhai Tian; Yadong Wang; Xiaohua Tony Hu; Qinghua Jiang; Jiangning Song; Shinichi Morishita; Kevin Burrage; Guohua Wang. Institute of Electrical and Electronics Engineers Inc., 2017. p. 137-140 7822507 (Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016).

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

Pavlovikj, N, Begcy, K, Behera, S, Campbell, M, Walia, H & Deogun, JS 2017, Analysis of transcriptome assembly pipelines for wheat. in K Burrage, Q Zhu, Y Liu, T Tian, Y Wang, XT Hu, Q Jiang, J Song, S Morishita, K Burrage & G Wang (eds), Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016., 7822507, Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016, Institute of Electrical and Electronics Engineers Inc., pp. 137-140, 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016, Shenzhen, China, 12/15/16. https://doi.org/10.1109/BIBM.2016.7822507
Pavlovikj N, Begcy K, Behera S, Campbell M, Walia H, Deogun JS. Analysis of transcriptome assembly pipelines for wheat. In Burrage K, Zhu Q, Liu Y, Tian T, Wang Y, Hu XT, Jiang Q, Song J, Morishita S, Burrage K, Wang G, editors, Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016. Institute of Electrical and Electronics Engineers Inc. 2017. p. 137-140. 7822507. (Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016). https://doi.org/10.1109/BIBM.2016.7822507
Pavlovikj, Natasha ; Begcy, Kevin ; Behera, Sairam ; Campbell, Malachy ; Walia, Harkamal ; Deogun, Jitender S. / Analysis of transcriptome assembly pipelines for wheat. Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016. editor / Kevin Burrage ; Qian Zhu ; Yunlong Liu ; Tianhai Tian ; Yadong Wang ; Xiaohua Tony Hu ; Qinghua Jiang ; Jiangning Song ; Shinichi Morishita ; Kevin Burrage ; Guohua Wang. Institute of Electrical and Electronics Engineers Inc., 2017. pp. 137-140 (Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016).
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