This pipeline is not maintained anymore but should be functional. It is a short-read quality control pipeline from the Sequana project. We would recommend to use the fastqc, demultiplex, and multitax pipelines instead.

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, remove phix and adapters + taxonomy
Status:	production. not maintained. Please use sequana_fastqc and sequana_multitax pipeline instead
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

Installation

You must install Sequana first:

pip install sequana

Then, just install this package:

pip install sequana_quality_control

Usage

sequana_quality_control --help
sequana_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.

Requirements

This pipelines requires the following executable(s):

• fastqc
• bwa
• sambamba
• samtools
• pigz
• cutadapt [or atropos]

Details

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.

ChangeLog

Version	Description
0.11.0	switch to click, pyproject. remove kraken (see multitax pipeline instead)
0.10.0	add missing MANIFEST
0.9.0	remove design_file for cutadapt to reflect changes in sequana 0.12.0 update kraken rules to use a kraken2 version Update to use new sequana framework (0.12) added CI action
0.8.4	fix the onsuccess section to reflect changes in sequana 0.9.3
0.8.3	fix cleaning output files
0.8.2	fix typo in parameter (-skip-phix-removal --> --skip-phix-removal) implement hiearchical kraken analysis. Required major updates of the sequana kraken rules + general fixes in sequana
0.8.1	uses more sequana tools to handle the options