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MetaSUB Quality Control Pipeline

This pipeline is deprecated Its functionality has been moved into the MetaSUB CAP.

This is the quality control pipeline used by MetaSUB. It has two steps
  • remove low quality bases and adapters from reads
  • rapidly align reads to the human genome and filter those that map

This pipeline is under heavy development. Most of the documentation for this pipeline is currently internal to MetaSUB.

Installation

This is a ModuleUltra Pipeline. For more information on installing ModuleUltra Pipelines see the main MetaSUB_CAP repo.

Running

To run the QC pipeline use the following commands

cd /analysis/dir
python /path/to/MetaSUB_CAP/add_fastq_data_to_datasuper.py <sample_type> [<fastq files>...]
moduleultra run -p metasub_qc_cap -j <njobs> [--dryrun]

To see more options just use the help commands

moduleultra run --help
moduleultra --help
datasuper --help

Most cluster systems will need a custom submit script. You can set a default script using the following command

moduleultra config cluster_submit /path/to/submit_script

Licence

MIT License