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StringTie

  • Description

    a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. Its input can include not only the alignments of raw reads used by other transcript assemblers, but also alignments longer sequences that have been assembled from those reads. In order to identify differentially expressed genes between experiments, StringTie's output can be processed by specialized software like Ballgown, Cuffdiff or other programs (DESeq2, edgeR, etc.).

  • Usage

    To list all executables provided by StringTie, run: $ biogrids-list stringtie Copy to clipboard

  • Installation

    Use the following command to install this title with the CLI client: $ biogrids-cli install stringtie Copy to clipboard Available operating systems: Linux 64, OS X INTEL

  • Primary Citation*

    M. Pertea, G. M. Pertea, C. M. Antonescu, T. C. Chang, J. T. Mendell, and S. L. Salzberg. 2015. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nature Biotechnology. 33: 290-295.


    • *Full citation information available through

  • Keywords

    RNA-Seq Analysis, Transcriptomics

  • Default Versions

    Linux 64:  2.2.1 (181.0 MB)
    OS X INTEL:  2.2.1 (123.5 MB)

  • Other Versions

      Linux 64:

      1.3.4 (4.5 MB) , 2.0.6 (5.5 MB) , 2.1.5 (6.4 MB)

    • OS X INTEL:

      1.3.4 (799.6 KB) , 2.0.6 (909.2 KB) , 2.1.5 (1.0 MB)

  • Developers

    Geo Pertea, Mihaela Pertea

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