- Python version:
Python 2.7, 3.4 and 3.5
- Online documentation:
- Issues and bug reports:
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
# contaminant and adapter removal search
from sequana import biomics
pipeline = biomics.Biomics("*fastq.gz") # assumm two paired-end fastq files
pipeline.create()
pipeline.start()
pipeline.report()
Behind the scene, a Snakefile and a config file are created in the local directory. The snakefile can be executed indepedently:
snakemake Snakefile -p
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