AutoInterOp
Description
Automatically runs a number of Illumina InterOp processing tools on a target MiSeq run folder. The folder should contain both an InterOp folder and a RunInfo.xml file.
Installation
pip3 install AutoInterOp
Dependencies
- InterOp==v1.1.2: https://github.com/Illumina/interop/releases/download/v1.1.2/InterOp-1.1.2-Linux-GNU.tar.gz
- gnuplot (
sudo apt install gnuplot)
NOTE: All InterOp binaries must be added to your $PATH.
Usage
Usage: AutoInterOp.py [OPTIONS]
Options:
-r, --run_folder PATH Path to an Illumina MiSeq run folder. This should
contain a SampleInfo.xml file and an InterOp
folder. [required]
-o, --output_folder PATH Path to desired output folder. Defaults to the
same place as the specified run_folder.
-z, --zip Set this flag to zip all output files into a
single archive available within your output folder.
--help Show this message and exit.
