sequana 0.1.0

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

pip install sequana

Some dependencies required include matplotlib, pandas, cutadapt, pysam. If you are new or starting with Python, we strongly recommand to use anaconda and to install those dependencies:

conda install matplotlib pandas cutadapt pysam

although the code is Python2.7 and Python3.5 compatible, a dependency (Snakemake) only supports Python3.5 for the moment so, we will assume you have a Python3.5 version installed.

Example

WIP but one component will be to have a set of rules available and ready to use in Snakefiles

# contaminant and adapter removal search
from sequana import snakemake
snakemake.rules()

In a snakefile:

from sequana import snakemake as sm
include: sm.rules['dag']