OmicsExplorer

OmicsExplorer is a bioinformatics workflow for genomics data generation and analysis an this GitHub contains a workflow for generating and exploring usefull data derived from 'omics'.

The aim of this workflow is to make knowledge out of data and the end point of this workflow should be to have a usable workflow for multiple kinds of omics layers, which a normally used to understand host-microbe interactions, as described in Limborg et al., 2017.

But please behold! This workflow is still under construction.

The OmicsExplorer workflow

General usage of OmicsExplorer - genomics and metagenomics

The OmicsExplorer workflow is based on a snakemake. This snakemake is based on a repository, which should be cloned from here. The first input of the workflow, should start from a repository, called 00_RawData. 00_RawData should contain raw fq.gz per sample. Importantly, all samples should have the postfix fq.gz and not fastq.gz, since the snakemake only recgonises fq.gz.

OmicsExplorer genome-resolved metagenomics workflow relies on anvi'o

The metagenomic part of OmicsExplorer is based a lot on the amazing platform anvi'o. All credits should be given to the anvi'o team!

Using OmicsExplorer and sbatch on a cluster

Since the OmicsExplorer is relying on some heavy computing, I have chosen to setup scripts to launch the snakemake in the sbatch submission system. These script has the prefix launch. The script will generate the necessary config.yaml file for the snakemake, based on information from the launch script, which should be defined before running the workflow.

Installation of conda environment and dependencies for OmicsExplorer

I base this workfol on conda and therefore miniconda should be installed prior the installation, please see link: https://docs.conda.io/en/latest/miniconda.html

First thing we need to do is, creating a conda environment. For this you will a config file with all dependencies. This file has already been made and can be downloaded here. It is called OmixExplorer.yml.

But else this code chunk should work for most people.

wget https://raw.githubusercontent.com/JacobAgerbo/OmicsExplorer/main/install_OE.sh
bash install_OE.sh

This environment has installed dependencies for for processing genomic data. Furthermore, it contains R (>4.1) with several packages, which are dependencies for shiny package, which are great for a fast overview of multivariate analysis.

After this you should be golden! And should be able launch the shiny app within R simply by typing:

QuickFixR::QuickFix()

QuickFixR can be used for any multivariate analysis, so please don't hesitate to use it for any analysis. Please find more info for QuickFixR on: https://github.com/JacobAgerbo/QuickFixR