sequana-quality-control 0.8.0

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 projet

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

Installation

You must install Sequana first:

pip install sequana

Then, just install this package:

pip install sequana_quality_control

Usage

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.

Requirements

This pipelines requires the following executable(s):

• fastqc

• bwa

• kraken (optional)

• krona (optional)

• 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.