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
This is is the quality_control pipeline from the Sequana project
|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|
|Input:||Raw fastq files|
|Output:||Cleaned fastQ files + taxonomy|
|Status:||production but meant to be simplified/changed in the near future (2020).|
|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|
You must install Sequana first:
pip install sequana
Then, just install this package:
pip install sequana_quality_control
sequana_pipelines_quality_control --help sequana_pipelines_quality_control --input-directory DATAPATH
This creates a directory with the pipeline and configuration file. You will then need to execute the pipeline:
cd quality_control sh quality_control.sh # for a local run
This launch a snakemake pipeline. If you are familiar with snakemake, you can retrieve the pipeline itself and its configuration files and then execute the pipeline yourself with specific parameters:
snakemake -s quality_control.rules -c config.yaml --cores 4 --stats stats.txt
Or use sequanix interface.
This pipelines requires the following executable(s):
- kraken (optional)
- krona (optional)
- cutadapt [or atropos]
This pipeline runs quality_control in parallel on the input fastq files (paired or not). A brief sequana summary report is also produced.
Rules and configuration details
Here is the latest documented configuration file to be used with the pipeline. Each rule used in the pipeline may have a section in the configuration file.
0.8.1: uses more sequana tools to handle the options
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
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|Filename, size sequana_quality_control-0.8.1.tar.gz (489.9 kB)||File type Source||Python version None||Upload date||Hashes View hashes|
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