Transposome

Transposome is a software tool developed to efficiently annotate transposable elements (TEs) from low-coverage whole-genome shotgun (WGS) data. It offers significant improvements in run time and produces more precise estimates of genomic repeat abundance compared to other annotation methods. Transposome is implemented in Perl and is freely available for download, and can also be used as a general toolkit for working with Next Generation Sequencing (NGS) data and for constructing custom genome analysis pipelines.

Topic

DNA;Mobile genetic elements;Genomics

Detail

  • Operation: Transposon prediction;Sequence annotation

  • Software interface: Command-line user interface

  • Language: C++

  • License: MIT License

  • Cost: Free

  • Version name: v0.12.1

  • Credit: National Science Foundation, USDA National Institute of Food and Agriculture

  • Input: -

  • Output: -

  • Contact: statonse@biodiversity.ubc.ca statonse@biodiversity.ubc.ca

  • Collection: -

  • Maturity: Stable

Publications

  • Transposome: a toolkit for annotation of transposable element families from unassembled sequence reads.
  • Staton SE and Burke JM. Transposome: a toolkit for annotation of transposable element families from unassembled sequence reads. Transposome: a toolkit for annotation of transposable element families from unassembled sequence reads. 2015; 31:1827-9. doi: 10.1093/bioinformatics/btv059
  • https://doi.org/10.1093/bioinformatics/btv059
  • PMID: 25644271
  • PMC: -

Download and documentation

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