RNA-Seq Analysis Pipeline Based on Oshell Environment
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 deve...
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| Veröffentlicht in: | IEEE/ACM transactions on computational biology and bioinformatics 2014-09, Vol.11 (5), p.973-978 |
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| container_title | IEEE/ACM transactions on computational biology and bioinformatics |
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| creator | Jing Li Jun Hu Newman, Matthew Kejun Liu Huanying Ge |
| description | 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. |
| doi_str_mv | 10.1109/TCBB.2014.2321156 |
| format | Article |
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| subjects | Bioinformatics Biology Clusters Computation Computational biology Computational Biology - methods Data processing Gene Expression Profiling - methods Genomics Junctions Linux Pipelines Quality control Sequence Alignment - methods Sequence Analysis, RNA - methods Sequencing Software Windows (computer programs) |
| title | RNA-Seq Analysis Pipeline Based on Oshell Environment |
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