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Sequana documentation

,

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 <Pipelines> dedicated to NGS in the form of Snakefiles (Makefile-like with Python syntax based on snakemake framework).
  3. Original tools to help in the creation of such pipelines including HTML reports.
  4. Standalone applications<applications>:
    1. sequana_coverage<standalone_sequana_coverage> ease the extraction of genomic regions of interest and genome coverage information
    2. sequana_taxonomy<standalone_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)

The sequana pipelines are various. Since March 2020, they have their own independent life within dedicated github repositories. You may find pipelines for NGS quality control (e.g. adapters removal, phix removal, trimming of bad quality bases), variant calling, characterisation of the genome coverage, taxonomic classification, de-novo assembly, Variant calling <pipeline_vc>, RNA-seq <pipeline_rnaseq>, etc. See the pipelines section for more information.

Sequana can be used by developers to create new pipelines and by users in the form of applications ready for production. Moreover, Sequanix can be used to set the parameters of pipelines and execute them easily with a graphical user interface.

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

Installation

conda install sequana

Examples

Visit our example gallery to use the Python library

NGS pipelines

Learn about available Snakemake pipelines

Standalone applications

Standalone applications including Sequanix (GUI for snakemake) and the sequana_coverage tool.

  • coverage
  • fastqc
  • kraken
  • bam
  • sequanix
  • pacbio

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User guide and reference

installation.rst userguide tutorial pipelines auto_examples/index case_examples applications sequanix.rst developers wrappers references references_enrich references_stats references_viz faqs glossary

Indices and tables

  • genindex
  • modindex
  • search