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Supported Applications

Subread

  • Description

    comprises a suite of software programs for processing next-gen sequencing read data including

    - Subread: a general-purpose read aligner which can align both genomic DNA-seq and RNA-seq reads. It can also be used to discover genomic mutations including short indels and structural variants.
    - Subjunc: a read aligner developed for aligning RNA-seq reads and for the detection of exon-exon junctions. Gene fusion events can be detected as well.
    - featureCounts: a software program developed for counting reads to genomic features such as genes, exons, promoters and genomic bins.
    - Sublong: a long-read aligner that is designed based on seed-and-vote.
    - exactSNP: a SNP caller that discovers SNPs by testing signals against local background noises.

  • Usage

    To list all executables provided by Subread, run: $ biogrids-list subread Copy to clipboard

  • Installation

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

  • Primary Citation*

    Y. Liao, G. K. Smyth, and W. Shi. 2013. The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote. Nucleic Acids Res.. 1(10): e108.


    • *Full citation information available through

  • Keywords

    High-throughput sequencing

  • Default Versions

    Linux 64:  2.0.3 (138.4 MB)
    OS X INTEL:  2.0.3 (80.2 MB)

  • Other Versions

      Linux 64:

      1.6.3 (110.8 MB)

    • OS X INTEL:

      1.6.3 (77.6 MB)
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