Supported Applications

Trimmomatic

  • Description

    a flexible read trimming tool for Illumina NGS data.

  • Usage Notes

    The alias trimmomatic may be used in place of the full command java -jar trimmomatic-0.35.jar

    For example, to run this command within the BioGrids environment:

    java -jar trimmomatic-0.35.jar SE -phred33 input.fq.gz output.fq.gz ILLUMINACLIP:TruSeq3-SE:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

    use the alias:

    trimmomatic SE -phred33 input.fq.gz output.fq.gz ILLUMINACLIP:TruSeq3-SE:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

    Use of the alias ensures the proper java version is called.

  • Primary Citation*

    A. M. Bolger, M. Lohse, and B. Usadel. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 30(15): 2114-2120.


    • *Full citation information available through

  • Keywords

    Utilities

  • Default Versions

    Linux 64:  0.39
    OS X INTEL:  0.39

  • Other Available Versions

      Linux 64:

      0.36
    • OS X INTEL:

      0.36
  • Developers

    Anthony Bolger, Bjoern Usadel.
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