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RNA-Seq Analysis Pipeline Based on Oshell Environment | IEEE Journals & Magazine | IEEE Xplore

RNA-Seq Analysis Pipeline Based on Oshell Environment


Abstract:

Advances in transcriptome sequencing (RNA-Seq) have revolutionized the way to characterize and quantify transcripts. The breakthroughs in RNA-Seq technologies give rise t...Show More

Abstract:

Advances in transcriptome sequencing (RNA-Seq) have revolutionized the way to characterize and quantify transcripts. The breakthroughs in RNA-Seq technologies give rise to the ever-increasing volumes of data, making data processing the bottleneck of transcriptome research. It becomes crucial to develop an efficient analysis pipeline to automate RNA-Seq data analysis. Based on Oshell environment, we present here an ultra-fast and powerful RNA-Seq analysis pipeline for quality control, sequence alignment, variation detection, expression quantification and junction discovery. The pipeline runs on both Linux and Windows operating systems, with either stand-alone or cluster computing environment. Parallel computing is also supported for improved processing speed. Oshell is free for non-commercial use at http://omicsoft.com/oshell.
Published in: IEEE/ACM Transactions on Computational Biology and Bioinformatics ( Volume: 11, Issue: 5, 01 Sept.-Oct. 2014)
Page(s): 973 - 978
Date of Publication: 30 April 2014

ISSN Information:

PubMed ID: 26356868

References

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