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© Research
Publication :

Sequana: a set of snakemake NGS pipelines

Scientific Fields
Diseases
Organisms
Applications
Technique

Published in - 30 Aug 2017

Thomas Cokelaer, Dimitri Desvillechabrol, Rachel Legendre, Mélissa Cardon

J. Open Source Softw, 2 p352

Sequana is a Python-based software dedicated to the development of Next Generation Sequencing (NGS) pipelines. We use the Snakemake (Köster and Rahmann 2012) framework to design our pipelines, which eases the decomposition of pipelines into modular sub-units. We currently have 7 pipelines covering quality control, variant calling, long-reads quality, de-novo and RNA-seq analysis (see https://sequana. readthedocs. io for details). Our pipelines are associated with HTML reports based on JINJA templating and Javascript. The reports are used to store the results of a pipelines but also materials required to reproduce the results. Sequana is also a Python library that provides tools to perform various analysis tasks (eg, variant call filtering). Some of the library components provide original tools that are also available as standalone applications. For instance a fast taxonomic …

https://doi.org/10.21105/joss.00352