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      Next-generation transcriptome assembly.

      1 ,  
      Nature reviews. Genetics
      Springer Science and Business Media LLC

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          Abstract

          Transcriptomics studies often rely on partial reference transcriptomes that fail to capture the full catalogue of transcripts and their variations. Recent advances in sequencing technologies and assembly algorithms have facilitated the reconstruction of the entire transcriptome by deep RNA sequencing (RNA-seq), even without a reference genome. However, transcriptome assembly from billions of RNA-seq reads, which are often very short, poses a significant informatics challenge. This Review summarizes the recent developments in transcriptome assembly approaches - reference-based, de novo and combined strategies - along with some perspectives on transcriptome assembly in the near future.

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          Author and article information

          Journal
          Nat Rev Genet
          Nature reviews. Genetics
          Springer Science and Business Media LLC
          1471-0064
          1471-0056
          Sep 07 2011
          : 12
          : 10
          Affiliations
          [1 ] Lawrence Berkeley National Laboratory, DOE Joint Genome Institute, 2800 Mitchell Drive, MS100 Walnut Creek, California 94598, USA. jamartin@lbl.gov
          Article
          nrg3068
          10.1038/nrg3068
          21897427
          311e91e2-1f0f-4249-b052-d848adcc1730

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