HmnIllumina

Parse InterOp folder from Illumina run to keep useful informations.

Install

conda install -n bioconda hmnillumina

Usage

HmnIllumina \
  -i/--input <FOLDER> \
  -o/--output <FILE>

The --input argument refers to an output directory produced by an Illumina sequencer named like 20200101_M0000_* for a Miseq run. The directory must contains:

• a RunInfo.xml file.
• a RunParameters.xml file.
• an InterOp directory with at least these files: ErrorMetricsOut.bin, IndexMetricsOut.bin, QMetricsOut.bin, TileMetricsOut.bin.

The --output argument refers to a JSON file.
Undefined values are denoted by "" or "NA".

Test

pytest is required:

make test

Built with these main libraries

• interop - InterOp library
• rapidjson - Json library