Evaluating assembly pipeline for transcriptomes

Natasha Pavlovikj, Kevin Bogey, Sairam Behera, Malachy Cambell, Harkamal Walia, Jitender S. Deogun

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

Abstract

The gene expression and transcriptome analysis are currently some of the main focuses of research for great number of biologists. The assembly of raw sequence data to obtain a draft transcriptome is a multi-stage pipeline consisting of complex steps like data cleaning, contaminant removal, error correction, de novo assembly, redundancy removal, and assembly validation. In this paper we developed and tested five transcriptome assembly pipelines for wheat transcriptome by using different tools. The assemblers Velvet- Oases and Trinity which use multiple and single k- mer methods respectively are used for our pipeline. In addition to that, different tools are used in the process of data cleaning and redundancy removal. The analysis of the results obtained from the five different assemblies show that the transcripts generated from Velvet-Oases with multiple k-mev approach and Oases-M have higher alignment ratio with the reference TriFLDB wheat transcriptome dataset.

Original languageEnglish (US)
Title of host publicationProceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014
PublisherInternational Society for Computers and Their Applications
Pages163-168
Number of pages6
ISBN (Print)9781632665140
StatePublished - Jan 1 2014
Event6th International Conference on Bioinformatics and Computational Biology, BICOB 2014 - Las Vegas, NV, United States
Duration: Mar 24 2014Mar 26 2014

Publication series

NameProceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014

Conference

Conference6th International Conference on Bioinformatics and Computational Biology, BICOB 2014
CountryUnited States
CityLas Vegas, NV
Period3/24/143/26/14

Fingerprint

Transcriptome
Pipelines
Triticum
Redundancy
Cleaning
Gene Expression Profiling
Error correction
Gene expression
Gene Expression
Impurities
Research

ASJC Scopus subject areas

  • Information Systems
  • Health Informatics

Cite this

Pavlovikj, N., Bogey, K., Behera, S., Cambell, M., Walia, H., & Deogun, J. S. (2014). Evaluating assembly pipeline for transcriptomes. In Proceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014 (pp. 163-168). (Proceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014). International Society for Computers and Their Applications.

Evaluating assembly pipeline for transcriptomes. / Pavlovikj, Natasha; Bogey, Kevin; Behera, Sairam; Cambell, Malachy; Walia, Harkamal; Deogun, Jitender S.

Proceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014. International Society for Computers and Their Applications, 2014. p. 163-168 (Proceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014).

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

Pavlovikj, N, Bogey, K, Behera, S, Cambell, M, Walia, H & Deogun, JS 2014, Evaluating assembly pipeline for transcriptomes. in Proceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014. Proceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014, International Society for Computers and Their Applications, pp. 163-168, 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014, Las Vegas, NV, United States, 3/24/14.
Pavlovikj N, Bogey K, Behera S, Cambell M, Walia H, Deogun JS. Evaluating assembly pipeline for transcriptomes. In Proceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014. International Society for Computers and Their Applications. 2014. p. 163-168. (Proceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014).
Pavlovikj, Natasha ; Bogey, Kevin ; Behera, Sairam ; Cambell, Malachy ; Walia, Harkamal ; Deogun, Jitender S. / Evaluating assembly pipeline for transcriptomes. Proceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014. International Society for Computers and Their Applications, 2014. pp. 163-168 (Proceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014).
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