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 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 /preprocessing/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 -xvzf Sample1_isolate.tar.gz
For /preprocessing/preprocessing
, 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.
Warning
Before proceeding to any of the bioinformatics workflows, make sure you have good quality data. See /preprocessing/preprocessing
for more.
Download data preprocessing conda environment file </downloads/preprocessing.yaml>
and data preprocessing test dataset </downloads/Sample1_isolate.tar.gz>
Best practices for /assembly/genome_assembly
and /assembly/metagenomic_workflows
.
Download isolate assembly conda environment file </downloads/isolate_assembly.yaml>
and isolate assembly test dataset </downloads/Sample1_isolate.tar.gz>
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!
preprocessing/preprocessing
assembly/genome_assembly assembly/metagenomic_workflows
taxonomic_profiling/16S taxonomic_profiling/metagenomes taxonomic_profiling/zAMP
comparative_genomics/SNVs_metagenomics.rst comparative_genomics/zDB
transcriptomics/metatranscriptomics.rst transcriptomics/metatranscriptomics_metagenomics.rst
tnseq/tnseq.rst