HTGTS-Rep is a pipeline for comprehensive analysis of HTGTS-Rep-seq.


Step 1

Download HTGTS-Rep pipeline.

Step 2

If necessary, install Miniconda. Create development conda environment with

conda env create environment.yml

Activate the environment with

source activate HTGTSrep

Step 3

Download proper version of Igblast and replace programs in igblast_bin folder if your OS is not Linux-based.

Run pipeline

To run the pipeline, you should always activate HTGTS-Rep environment except you have all dependent softwares installed.

source activate HTGTSrep

Run the pipeline using subcommand "run" for V,D,J usage analysis.

python HTGTSrep.py run

Run the pipeline using subcommand "mut" for V gene mutation profiling.

python HTGTSrep.py mut