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.