Skip to main content

Long read amplicon analysis

Project description JOSS (journal of open source software) DOI

This is is the laa pipeline from the Sequana project


Perform amplicon analysis on Pacbio data sets including variant and phylogeny


A set of CCS files from pacbio in FastQ formats


variant calling, phylogney, consensus genomes, etc


production but may change


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

This pipeline was used in :


You must install Sequana first:

pip install sequana

Then, just install this package:

pip install sequana_laa


sequana_laa --help
sequana_laa --input-directory DATAPATH

This creates a directory with the pipeline and configuration file. You will then need to execute the pipeline:

cd laa
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 laa.rules -c config.yaml --cores 4 --stats stats.txt --wrapper-prefix git+file:///home/cokelaer/Work/github/forked/sequana-wrappers

Or use sequanix interface.


This pipelines requires the following executable(s):

  • vt

  • freebayes

  • igvtools

  • sequana

  • snpeff (optional)

  • samtools

  • bamtools

  • minimap2


This pipeline runs amplicon analysis on long reads data from pacbio sequencers.

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.





full integration with latest wrapeprs and apptainers from damona


add singularity containers


First release.

Download files

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

Source Distribution

sequana_laa-0.10.0.tar.gz (106.6 kB view hashes)

Uploaded source

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page