sequana-quality-control 0.10.0

Description:

sequanaqualitycontrol 0.10.0

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
kraken2 (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.


ChangeLog


Version
Description



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