Skip to main content

A fastqc pipeline from sequana project.

Project description JOSS (journal of open source software) DOI

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


You must install Sequana first (use –upgrade to get the latest version installed):

pip install sequana --upgrade

Then, just install this package:

pip install sequana_fastqc --upgrade


This command will scan all files ending in .fastq.gz found in the local directory, create a directory called fastqc/ where a snakemake pipeline is launched automatically. Depending on the number of files and their sizes, the process may be long:

sequana_fastqc --run

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_pipelines_fastqc --help
sequana_pipelines_fastqc --input-directory DATAPATH

This creates a directory fastq. You just need to execute the pipeline:

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)
  • sequana (Python: pip install sequana)

For Linux users, we provide a singularity image available through damona:

pip install damona
damona install fastqc
# and add the ~/.config/damona/bin path to your binary PATH


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.


Version Description
  • 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
0.9.6 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.

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

sequana_fastqc-1.4.2.tar.gz (89.6 kB view hashes)

Uploaded source

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring Facebook / Instagram Facebook / Instagram PSF Sponsor Fastly Fastly CDN Google Google Object Storage and Download Analytics Huawei Huawei PSF Sponsor Microsoft Microsoft PSF Sponsor NVIDIA NVIDIA PSF Sponsor Pingdom Pingdom Monitoring Salesforce Salesforce PSF Sponsor Sentry Sentry Error logging StatusPage StatusPage Status page