Optimizing the RNA-Seq transcriptome discovery pipeline for Aspergillus fumigatus

Ref ID: 18392

Author:

Suman Pakala, Vinita Joardar, Nikhat Zafar, Suchitra Pakala,
Sean Murphy, Natalie Fedorova and William Nierman J. Craig Venter Institute,

Author address:

Rockville, MD, USA. spakala@jcvi.org

Full conference title:

Asperfest 8

Abstract:

RNA-Seq has become invaluable to applicationssuch astranscript expression quantification and genome annotation, including discovery of non-coding
RNAs and identification of new gene models and isoforms. The continued evolution of deep sequencing technologies has resulted in active development
of new data analysis tools. It has become necessary for research groups to identify the appropriate set of tools that best suit their needs. As part of the
Aspergillus fumigatus re-annotation project, we sequenced several cDNA libraries using Illumina GA II and evaluated publicly available transcript
discovery approaches. Specifically, this comparison includes (i) the de novo transcript assembly approach, (ii) the alignment followed by assembly of
transcripts approach and also (iii) a hybrid approach for transcript identification. Performance of various short read aligners, splice junction mappers,
and transcript assemblers that implement these approaches have been evaluated. Based on this study, we present a general framework for evaluating RNASeq data analysis tools and discuss our results of such an evaluation and optimization of the analysis pipeline for the A. fumigatus genome

Abstract Number: 72)

Conference Year: 2011

Link to conference website: NULL

New link: NULL

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