Methods in Microbiomics
Set of guidelines and best practices for robust and reproducible bioinformatics processing and data analysis with the focus on Microbiomics research.
This documentation is currently under construction.
Tutorials are available for each section listed below. To start, create a directory for the tutorial of your interest:
For example, for Data Preprocessing, run:
For the next section, you have to install conda first. Installation instructions can be found here.
For each of the sections we have provided a link to a conda environment file (i.e. a file that specifies which packages to install) and a test dataset that can be used for practice. Download these files and save them to the tutorial directory. Next, you can create and activate the conda environment and extract the test data:
conda env create -f <environment name>.yaml
conda activate <environment name>
tar -xvzf Sample1_isolate.tar.gz
mamba env create -f isolate_assembly.yaml
conda activate isolate_assembly
tar -xvpf Sample1_isolate.tar.gz
Now, you are ready to run the example commands given in the corresponding section.
Before proceeding to any of the bioinformatics workflows, make sure you have good quality data. See Data Preprocessing for more.
Best practises for profiling of amplicon and metagenomic data
Best practices for transcriptomic and metatranscriptomic data analysis
Best practices in metagenomic data analysis
If you have any questions or suggestions leave a comment below!