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RNA-Seq Analysis Pipeline Based on Oshell Environment
PrePrint
ISSN: 1545-5963
Jing Li, J. Li is with Division of Bioinformatics, Omicsoft Corporation, 200 Cascade Pointe Lane, Suite 101, Cary, NC 27513.
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.
Citation:
Matthew Newman, Huanying Ge, Kejun Liu, Jing Li, Jun Hu, "RNA-Seq Analysis Pipeline Based on Oshell Environment," IEEE/ACM Transactions on Computational Biology and Bioinformatics, 22 May 2014. IEEE computer Society Digital Library. IEEE Computer Society, <http://doi.ieeecomputersociety.org/10.1109/TCBB.2014.2321156>
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