Biomics Dry-lab Group (2018-2024)

Biomics-Hub drylab Software development

Overview

We are involved in the Data management of the Biomics Platform dealing with hundreds of projects a year. We are also analysing some of those projects but even more importantly we design software.

In this page, we provide a very brief overview of what is been doing those days.

Damona

Damona is an initiative to create a singularity manager to easily install software. This is the software manager used within the Biomics platform. More information can be found here documentation

Sequana

Sequana is our NGS analysis framework used to perform all the in-house bioinformatics analysis

BioServices

BioServices is a Python library that gives access to tens of web services such as UniProt, Ensembl, etc

BioConvert

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.

Sequana

Sequana is the framework used within the Biomics platform to perfom all QCs and service analysis.

Here are some example of pipelines that are available. Full details can be found on https://sequana.readthedocs.io

RNA-seq

The RNA-seq pipeline is designed in Snakemake. This pipelin has beenused on hundreds of projects. and combined with Sequana can start from raw read up the GO and KEGG enrichments. documentation

This pipeline maps reads on a refernce and calls variants using freebayes. HTML reports allows the exploration of the variants found. This pipeline also provide the analysis of the mapping coverage using sequana coverage. documentation

Biomics Dry-lab Group (2018-2024)

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