# App TrainingSV: Biosphere BASE environment for SV analysis using Jupyter

## Description

This IFB cloud appliance provides both the Jupyter Notebook and Lab environment to work on the structural variants detections on short and long reads.

This Jupyter app is based on the Jupyter Docker Stacks. By default, this Biosphere app uses the stack jupyter/datascience-notebook but users can choose any other existing stack with an Advanced deployment in Biosphere portal.
In addition, we integrated various tools to perform the SV detection

## Tools

* [Bash kernel for jupyter](https://pypi.org/project/bash_kernel/)
* [Pandas](https://pypi.org/project/pandas/)
* [Matplotlib](https://pypi.org/project/matplotlib/)
* [Jupyter notebook/lab](https://jupyter.org)
* [seqtk](https://github.com/lh3/seqtk)
* [Minimap2](https://github.com/lh3/minimap2)
* [BWA-MEM2](https://github.com/bwa-mem2/bwa-mem2)
* [Samtools/BCFtools](http://www.htslib.org/)
* [BEDtools](https://bedtools.readthedocs.io/en/latest/)
* [VCFtools](https://vcftools.github.io/index.html)
* [GATK](https://gatk.broadinstitute.org/hc/en-us)
* [Syri](https://github.com/schneebergerlab/syri)
* [BreakDancer](https://github.com/genome/breakdancer)
* [Sniffles](https://github.com/fritzsedlazeck/Sniffles)
* [Mummer](https://github.com/mummer4/mummer)





## Contact

* [Support Cloud IFB](mailto:biosphere-support@genouest.org) 

## Developpers

* Francois Sabot [SouthGreen Platform](https://southgreen.fr)
* Julie Orjuela-Bouniol [SouthGreen Platform](https://southgreen.fr)


## App data

* Version : 20.04
* OS : Ubuntu
* OS version : 20.04

## Licence

Licensed under GPLv3