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Authors: Mark Onyango 1 ; Carsten Ade 2 ; Franz Cemič 1 and Jürgen Hemberger 1

Affiliations: 1 University of Applied Sciences Giessen, Germany ; 2 University of Würzburg, Germany

ISBN: 978-989-8565-35-8

Keyword(s): DGE, RNA-Seq, Pipeline, Differential Expression, Quality Assessment, Tag-Seq, shRNA.

Related Ontology Subjects/Areas/Topics: Algorithms and Software Tools ; Bioinformatics ; Biomedical Engineering ; Next Generation Sequencing ; Sequence Analysis

Abstract: With the development of next generation high-throughput sequencing solutions to expression profiling, the efficient and effortless handling of such profiling data became a key challenge for bioinformaticians and biologists alike. We therefore present a "fire and forget" style pipeline implemented in C and R, named QUASI. It is capable of quality assessments, sequence alignments, shRNA quantification and statistically inferring significant differential sequence abundance from datasets presented to it. Through blackboxing the often complex and laborious steps, QUASI presents itself as a user-friendly and time-efficient solution to handle pooled shRNA library screening data.

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Paper citation in several formats:
Onyango, M.; Ade, C.; Cemič, F. and Hemberger, J. (2013). QUASI: A Pipeline for the Quality Assessment and Statistical Inference on Next Generation Sequencing Data from Pooled shRNA Library Screens.In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2013) ISBN 978-989-8565-35-8, pages 288-291. DOI: 10.5220/0004220702880291

@conference{bioinformatics13,
author={Mark Onyango. and Carsten Ade. and Franz Cemič. and Jürgen Hemberger.},
title={QUASI: A Pipeline for the Quality Assessment and Statistical Inference on Next Generation Sequencing Data from Pooled shRNA Library Screens},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2013)},
year={2013},
pages={288-291},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0004220702880291},
isbn={978-989-8565-35-8},
}

TY - CONF

JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2013)
TI - QUASI: A Pipeline for the Quality Assessment and Statistical Inference on Next Generation Sequencing Data from Pooled shRNA Library Screens
SN - 978-989-8565-35-8
AU - Onyango, M.
AU - Ade, C.
AU - Cemič, F.
AU - Hemberger, J.
PY - 2013
SP - 288
EP - 291
DO - 10.5220/0004220702880291

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