Methods in Microbiomics

Set of guidelines and best practices for robust and reproducible bioinformatics processing and data analysis with the focus on Microbiomics research.

Important

This documentation is currently under construction.

Tutorials

Tutorials are available for each section listed below. To start, create a directory for the tutorial of your interest:

mkdir <section>_tutorial
cd <section>_tutorial

For example, for Data Preprocessing, run:

mkdir preprocessing_tutorial
cd preprocessing_tutorial

Note

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 -xvpf Sample1_isolate.tar.gz

For Genome Assembly, you need to install mamba. Here are the commands to create the conda environment and unpack the data:

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.

Data Preprocessing

Warning

Before proceeding to any of the bioinformatics workflows, make sure you have good quality data. See Data Preprocessing for more.

Download data preprocessing conda environment file and data preprocessing test dataset

Genome Assembly

Best practices for Genome Assembly and Metagenomic Assembly.

Download isolate assembly conda environment file and isolate assembly test dataset

Taxonomic Profiling

Best practises for profiling of amplicon and metagenomic data

Transcriptomics Analysis

Best practices for transcriptomic and metatranscriptomic data analysis

Best practices in metagenomic data analysis

Support

If you have any questions or suggestions leave a comment below!