A METTRE A JOUR

Microbiome Analysis Workflow

Author

Thomas Vannier (@metavannier), https://centuri-livingsystems.org/t-vannier/

About

This workflow performs a metabarcoding analysis from fastq files to the production of a report with result of the marker-gene analysis. The analysis are mainly been achieved using plugins from QIIME 2, Bolyen et al., 2019.

You need to install Singularity on your computer. This workflow also work in a slurm environment.

Each snakemake rules call a specific conda environment. In this way you can easily change/add tools for each step if necessary.

Usage

Step 1: Install workflow

You can use this workflow by downloading and extracting the latest release. If you intend to modify and further extend this workflow or want to work under version control, you can fork this repository.

We would be pleased if you use this workflow and participate in its improvement. If you use it in a paper, don't forget to give credits to the author by citing the URL of this repository and, if available, its [DOI](https://doi.org/to update).

Step 2: Configure workflow

Configure the workflow according to your needs via editing the files and repositories:

• 00_RawData need the fastq file of each run to analyse
• 01_Reference the Marker gene reference databases and the SEPP reference databases if you build the phylogenetic tree with SEPP.
• manifest.tsv, sample-metadata.tsv and conditions.tsv ans sample-filtered.tsv to indicate the samples, run, metadata, conditions and sample to remove for the analyse.
• config.yaml indicating the parameters to use.
• Comment the Snakefile on the input line not expected for the pipeline. This depend of the denoising, phylogenetic methods used and if longitudinal analysis are possible (to be improved).

Step 3: Execute workflow

• You need Singularity v3.5.3 installed on your computer or cluster.

• Load snakemake from a docker container and run the workflow from the root by using these commands:

singularity run docker://snakemake/snakemake:v6.3.0

• Then execute the workflow locally via

snakemake --use-conda --use-singularity --cores 10

Step 4: Investigate results

After successful execution, you can create a self-contained interactive HTML report with all results via:

snakemake --report report.html