Here we present a tool called iteres used for getting alignment statistics of transposable elements. A basic workflow of using this tool includes:

  1. Do reads alignment using bwa, generate .bam or .sam files.
  2. Using the .bam/.sam files generated above as input for iteres, generate TE subfamily statistics.

For paired-end sequencing data, make sure you generate the .bam/.sam in pair-end alignment mode. iteres will automatically detect paired-end or single-end alignment results.

For iteres installation, please see the Download page.

For full documentation, please visit the Documentation page.

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How does it work?

iteres was the sucessor of the Repeat Analysis Pipeline (RAP), also see the Nature Genetics paper: DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape for details about RAP. Following was the principle of iteres: