{"id":18448824,"url":"https://github.com/sequana/quality_control","last_synced_at":"2026-04-17T14:03:13.097Z","repository":{"id":43139501,"uuid":"228156131","full_name":"sequana/quality_control","owner":"sequana","description":"A quality control pipeline for illumina data set. 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It is a short-read quality control pipeline\nfrom the `Sequana \u003chttps://sequana.readthedocs.org\u003e`_ project. We would recommend to use the fastqc, demultiplex,\nand multitax pipelines instead.\n\n:Overview: A quality control pipeline for illumina data set. This pipeline removes contaminants (e.g. Phix), performs fastqc, adapter cleaning and trimming and checks for contaminants\n:Input: Raw fastq files\n:Output: Cleaned fastQ files, remove phix and adapters + taxonomy\n:Status: production. **not maintained**. Please use sequana_fastqc and sequana_multitax pipeline instead\n:Citation: Cokelaer et al, (2017), ‘Sequana’: a Set of Snakemake NGS pipelines, Journal of Open Source Software, 2(16), 352, JOSS DOI doi:10.21105/joss.00352\n\n\nInstallation\n~~~~~~~~~~~~\n\nYou must install Sequana first::\n\n    pip install sequana\n\nThen, just install this package::\n\n    pip install sequana_quality_control\n\n\nUsage\n~~~~~\n\n::\n\n    sequana_quality_control --help\n    sequana_quality_control --input-directory DATAPATH\n\nThis creates a directory with the pipeline and configuration file. You will then need\nto execute the pipeline::\n\n    cd quality_control\n    sh quality_control.sh  # for a local run\n\nThis launch a snakemake pipeline. If you are familiar with snakemake, you can\nretrieve the pipeline itself and its configuration files and then execute the pipeline yourself with specific parameters::\n\n    snakemake -s quality_control.rules -c config.yaml --cores 4 --stats stats.txt\n\nOr use `sequanix \u003chttps://sequana.readthedocs.io/en/master/sequanix.html\u003e`_ interface.\n\nRequirements\n~~~~~~~~~~~~\n\nThis pipelines requires the following executable(s):\n\n- fastqc\n- bwa\n- sambamba\n- samtools\n- pigz\n- cutadapt [or atropos]\n\n.. image:: https://raw.githubusercontent.com/sequana/quality_control/master/sequana_pipelines/quality_control/dag.png\n\n\nDetails\n~~~~~~~\n\nThis pipeline runs **quality_control** in parallel on the input fastq files (paired or not).\nA brief sequana summary report is also produced.\n\n\nRules and configuration details\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\nHere is the `latest documented configuration file \u003chttps://raw.githubusercontent.com/sequana/sequana_quality_control/master/sequana_pipelines/quality_control/config.yaml\u003e`_\nto be used with the pipeline. Each rule used in the pipeline may have a section in the configuration file.\n\nChangeLog\n~~~~~~~~~\n\n\n========= ====================================================================\nVersion   Description\n========= ====================================================================\n0.11.0    * switch to click, pyproject. remove kraken (see multitax pipeline\n            instead)\n0.10.0    * add missing MANIFEST\n0.9.0     * remove design_file for cutadapt to reflect changes in\n            sequana 0.12.0\n          * update kraken rules to use a kraken2 version\n          * Update to use new sequana framework (0.12)\n          * added CI action\n0.8.4     * fix the onsuccess section to reflect changes in sequana 0.9.3\n0.8.3     * fix cleaning output files\n0.8.2     * fix typo in parameter (-skip-phix-removal --\u003e --skip-phix-removal)\n          * implement hiearchical kraken analysis. Required major updates of\n            the sequana kraken rules + general fixes in sequana\n0.8.1     uses more sequana tools to handle the options\n========= ====================================================================\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsequana%2Fquality_control","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsequana%2Fquality_control","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsequana%2Fquality_control/lists"}