This is is the fastqc pipeline from the Sequana projet

Overview

Runs fastqc and multiqc on a set of Sequencing data to produce control quality reports

Input

A set of FastQ files (paired or single-end) compressed or not

Output

An HTML file summary.html (individual fastqc reports, mutli-samples report)

Status

Production

Wiki

https://github.com/sequana/fastqc/wiki

Documentation

This README file, the Wiki from the github repository (link above) and https://sequana.readthedocs.io

Citation

Cokelaer et al, (2017), 'Sequana': a Set of Snakemake NGS pipelines, Journal of Open Source Software, 2(16), 352, JOSS DOI https://doi:10.21105/joss.00352

sequana_fastqc is based on Python3, just install the package as follows:

pip install sequana_fastqc --upgrade

You will need third-party software such as fastqc. Please see below for details.

If you have a set of FastQ files in a data/ directory, type:

sequana_fastqc --input-directory data

To know more about the options (e.g., add a different pattern to restrict the execution to a subset of the input files, change the output/working directory, etc):

sequana_fastqc --help

The call to sequana_fastqc creates a directory fastqc. Then, you go to the working directory and execute the pipeline as follows:

cd fastqc
sh fastqc.sh  # for a local run

This launch a snakemake pipeline. If you are familiar with snakemake, you can retrieve the fastqc.rules and config.yaml files and then execute the pipeline yourself with specific parameters:

snakemake -s fastqc.rules --cores 4 --stats stats.txt

Or use sequanix interface.

Please see the Wiki for more examples and features.

You can retrieve test data from sequana_fastqc (https://github.com/sequana/fastqc) or type:

wget https://raw.githubusercontent.com/sequana/fastqc/master/sequana_pipelines/fastqc/data/data_R1_001.fastq.gz
wget https://raw.githubusercontent.com/sequana/fastqc/master/sequana_pipelines/fastqc/data/data_R2_001.fastq.gz

then, prepare the pipeline:

sequana_fastqc --input-directory .
cd fastqc
sh fastq.sh

# once done, remove temporary files (snakemake and others)
make clean

Just open the HTML entry called summary.html. A multiqc report is also available. You will get expected images such as the following one:

Please see the Wiki for more examples and features.

This pipelines requires the following executable(s):

• fastqc
• falco (optional)

For Linux users, we provide apptainer/singularity images available through the damona project (https://damona.readthedocs.io).

To make use of them, initiliase the pipeline with the --use-apptainer option and everything should be downloaded automatically for you, which also guarantees reproducibility:

sequana_fastqc --input-directory data --use-apptainer --apptainer-prefix ~/images

This pipeline runs fastqc in parallel on the input fastq files (paired or not) and then execute multiqc. A brief sequana summary report is also produced. s You may use falco instead of fastqc. This is experimental but seem to work for Illumina/FastQ files.

This pipeline has been tested on several hundreds of MiSeq, NextSeq, MiniSeq, ISeq100, Pacbio runs.

It produces a md5sum of your data. It copes with empty samples. Produces ready-to-use HTML reports, etc

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.

To contribute to this project, please take a look at the Contributing Guidelines first. Please note that this project is released with a Code of Conduct. By contributing to this project, you agree to abide by its terms.