sequana 0.1.1

Put a short description here

Python version:

Python 2.7, 3.4 and 3.5

Online documentation:

On readthedocs

Issues and bug reports:

On github

Sequana includes a set of pipelines related to NGS (new generation sequencing).

It will provide a set of modular pipelines and reports associated to them.

Installation

If you already already install dependencies, this should install the latest release:

pip install sequana --upgrade

Some dependencies required include matplotlib, pandas, cutadapt, pysam. If you are new or starting with Python, we strongly recommand you to use anaconda. We use the bioconda channel, which can be added to your environment as follows:

conda config --add channels r
conda config --add channels bioconda

Then, install those dependencies:

conda install numpy matplotlib pandas cutadapt pysam bwa bcftools pyvcf samtools snakemake biokit bioservices bedtools picard freebayes

although the code is Python2.7 and Python3.5 compatible, a dependency (Snakemake) only supports Python3.5 for the moment so we will support only Python3.5 version. If you wish to use functionalities of Sequana that do not make use of Snakemake, you may still used it with Python2.7.

Developers can also install other tols:

conda install nose coverage

Please see the documentation for usage and examples