Utility to transform UMI's in Illumina fastq headers to UMI in separate tags. Outputs a new (interleaved) fastq file. This tool was built to parse output from Illumina bcl-convert where the "OverrideCycles" option was used.
pip install git+https://github.com/CenterForMedicalGeneticsGhent/UMInizer.git
or
python setup.py install
UMInizer fastq_R1.fastq.gz fastq_R2.fastq.gz | bgzip -c > interleaved.fastq.gz