- Runs bcl2fastq on Illumina sequencer output with settings inferred from ELM (if not overwritten manually)
- MUXes are processed in parallel and each has it's own folder (i.e.
./out/Project_<MUX>) - Each MUX component library has its own sub-folder (e.g.
./out/Project_<MUX>/Sample_<lib>) - In addition, FastQC is run on each fastq file
End-users will not want to use this pipeline!
The directory contains auxiliary scripts used for production operations only.