edwardslab/tedetective repository overview

Container for running TE-Detective⁠, which detects TE insertions in short-read sequencing data.

Includes all requirements for running TE-Detective including censor, ncbi-blast, bwa, anaconda3, and the python modules pysam, numpy, and biopython.

Be sure the following are added to your PATH:

   /opt/anaconda3/bin/
   /usr/local/bwa
   /usr/local/blast-2.2.26/bin

Set the environmental variable:

BLASTDIR=/usr/local/blast-2.2.26/bin

A simple example is included at:

   /usr/local/TE-detective/TEdetective_example.tar.gz

See simple example instructions on the TE-detective github page⁠ for more information.