Pan_TE

Design for linear or graph genome TE detection and classification

Software Installation

1.Download the latest Pipeline:

git clone https://github.com/unavailable-2374/Pan_TE.git

2.Install:

cd Pan_TE
chmod 750 bin/*
export PATH=/YOUR/PATH/TO/bin //* like: export PATH=/public/home/soft/Pan_TE/bin:$PATH
mamba env create -f env/pgta.yml
ln -s /PATH/TO/miniconda3/envs/PGTA/bin/x86_64-conda-linux-gnu-g++ /PATH/TO/miniconda3/envs/PGTA/bin/g++
conda activate PGTA

Look4LTRs intallation section:

git clone https://github.com/BioinformaticsToolsmith/Look4LTRs.git
cd Look4LTRs
mkdir bin
cd bin
cmake ..
vim ../src/Util.h add "#include <cstdint>" on the top
vim ../src/KmerHistogram.h add "#include <cstdint>" on the top
make look4ltrs
export PATH=/YOUR/PATH/TO/Look4LTRs/bin:$PATH

ClassifyTE intallation section:

git clone https://github.com/manisa/ClassifyTE.git

go to this link

• Click on ClassifyTE_Models.zip. This will automatically download models built with TE datasets.
• Unzip and copy all the models from "ClassifyTE_Models" directory into the folder model inside the root folder ClassifyTE

Usage:

Parameters:
[General]
    --genome <string>         Required. Genome file in FASTA format.
    --ClassifyTE_dir <string> Provide path to ClassifyTE for classification.
    --RM_dir <string>         Provide path to rmblastn for classification.

[Other]
    --list <string>           Default: NA. Path file for GFA, see gfa.list for format.
    --out <string>            Default: current directory. The work directory.
    -M <int>                  Memory limit (in MB), default: 0 (unlimited).
    --flag <string>           PGGB or Minigraph-Cactus.
    --cpu <int>               Default: 4. Number of threads, preferably in multiples of 4.
    --fragment_size <int>     Default: 40000. Length for fragment.
    --help|-h                 Display this help information.

Version: 1.0.0 USAGE