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A multi-sample fastqc pipeline from Sequana project

Project description JOSS (journal of open source software) DOI Python 3.8 | 3.9 | 3.10

This is is the fastqc pipeline from the Sequana projet


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


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


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





This README file, the Wiki from the github repository (link above) and


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  # 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 ( or type:


then, prepare the pipeline:

sequana_fastqc --input-directory .
cd fastqc

# 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 (

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

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.





  • uses pyproject instead of setuptools

  • uses click instead of argparse and newest sequana_pipetools (0.16.0)


  • Set wrapper version in the config based on new sequana_pipetools feature


  • Use new rulegraph wrapper and new graphviz apptainer


  • slight refactorisation to use rulegraph wrapper


  • pin sequana version to 1.4.4 to force usage of new fastqc module to fix falco. Updated config documentation.


  • Fixed falco output error and use singularity containers


  • removed modules completely.


  • simplified pipeline (suppress setup and use existing wrapper)


  • simplified pipeline with wrappers/rules


  • This version uses sequana 0.12.0 and new sequana-wrappers mechanism. Functionalities is unchanged. Also based on sequana_pipetools 0.6.X


  • add option –skip-multiqc (in case of memory trouble)

  • Fix typo in the link towards fastqc reports in the summary.html table

  • Fix number of samples in the paired case (divide by 2)


  • compatibility with Sequanix

  • Fix pipeline to cope with new snakemake API


  • add new rule to allow users to choose falco software instead of fastqc. Note that fastqc is 4 times faster but still a work in progress (version 0.1 as of Nov 2020).

  • allows the pipeline to process pacbio files (in fact any files accepted by fastqc i.e. SAM and BAM files

  • More doc, test and info on the wiki


  • add md5sum of input files as md5.txt file


  • a stable version. Added a wiki on github as well and a singularity recipes


  • For the HTML reports, takes into account samples with zero reads


  • round up some statistics in the main table


  • improve the summary HTML report


  • implemented new –from-project option


  • now depends on sequana_pipetools instead of sequana.pipelines to speed up –help calls

  • new summary.html report created with pipeline summary

  • new rule (plotting)


  • simplify the onsuccess section


  • add missing png and pipeline (regression bug)


  • add missing multi_config file


  • check existence of input directory in

  • add a logo

  • fix schema

  • add multiqc_config

  • add sequana + sequana_fastqc version


add the readtag option

Contribute & Code of Conduct

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.

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