Skip to main content

A fastqc pipeline from sequana project.

Project description

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 index.html (multiqc) and tree.html (individual fastqc report)
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:

pip install sequana

Then, just install this package:

pip install sequana_fastqc


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.


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 index.html and browse the multiqc report. For individual reports, open the tree.html file. You will get expected images such as the following one:


This pipelines requires the following executable(s):

  • fastqc


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.

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
  • 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

Download files

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

Files for sequana-fastqc, version 0.9.13
Filename, size File type Python version Upload date Hashes
Filename, size sequana_fastqc-0.9.13.tar.gz (66.8 kB) File type Source Python version None Upload date Hashes View

Supported by

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