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Sequana bioconvert pipeline documentation

|version|, |today|, status: production

The bioconvert pipeline is a Sequana pipeline. You can find the source code on https://github.com/sequana/sequana_bioconvert. Would you have issues about the code, usage or lack of information, please fill a report on Sequana itself indicating the pipeline name (We centralized all pipelines issues on Sequana repository only so as to be more responsive).

If you use Sequana, please do not forget to cite us:

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

The Sequana bioconvert pipeline

What is Sequana ?

Sequana is a versatile tool that provides

  1. A Python library dedicated to NGS analysis (e.g., tools to visualise standard NGS formats).
  2. A set of Pipelines dedicated to NGS in the form of Snakefiles
  3. Standalone applications
    1. sequana_coverage ease the extraction of genomic regions of interest and genome coverage information
    2. sequana_taxonomy performs a quick taxonomy of your FastQ. This requires dedicated databases to be downloaded.
    3. Sequanix, a GUI for Snakemake workflows (hence Sequana pipelines as well)

To join the project, please let us know on github.

For more information, please see github.