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Project description
- Python version:
Python 2.7 and 3.5
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Sequana includes a set of pipelines related to NGS (new generation sequencing) including quality control, variant calling, coverage, taxonomy.
Please see the documentation for usage and examples
Installation
The installation process is explained in the documentation but here is a quick explanation. If you have already installed Sequana dependencies, this command should install the latest release posted on Pypi website:
pip install sequana --upgrade
There are a few dependencies that needs to be compiled (time consumming and requires proper C compilator). For instance, we use Matplotlib, Pandas, cutadapt but some pipelines also require more specific tools (e.g. BWA for read alignment). We therefore strongly recommend to use Anaconda and in particular the bioconda channel, which can be added to your environment as follows (once Anaconda is installed):
conda config --add channels r conda config --add channels bioconda
Here is a non exhaustive list of dependencies that should be enough to run the current pipelines (version 0.1.4). We split the command on several lines to emphasize the standard Anaconda packages and te bioconda ones but you can use only one:
conda install numpy matplotlib pandas cutadapt pysam pyvcf snakemake biokit bioservices conda install bwa bcftools samtools bedtools picard freebayes fastqc
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