The tutorial is designed for researchers on focused metagenomics (WGS/shotgun) data analysis who are interested in developing or customizing taxonomic annotation pipelines. It builds on the Hello Nextflow and Nextflow for RNAseq beginner training and demonstrates how to use Nextflow in the specific context of metagenomics data analysis.
Specifically, this tutorial demonstrates how to implement a simple read taxonomic annotation starting from removing host sequences, passing through re-estimating species abundance with Bayesian statistics, until generating complete reports.
To start, please go to the official website of the tutorial: https://taxoflow.work/
By the end of this tutorial, you will have learnt how to apply foundational Nextflow concepts and tooling to a typical metagenomics use case.
Concretely, you will be able to:
- Write a linear workflow to perform host removal, taxonomic annotation and species abundance re-estimation
- Handle domain-specific files such as Kraken2 and Bracken reports resources appropriately
- Run analysis for a single sample or leverage on Nextflow's dataflow paradigm to parallelize multi-sample analysis
- Separate the processes and workflow in a more structured manner attempting to a first step in following nf-core guidelines
- Use conditionals and operators to control workflow execution
- Include custom scripts to be run within a given process
The tutorial assumes some minimal familiarity with the following:
- Tools and file formats commonly used in this scientific domain
- Experience with the command line
- Foundational Nextflow concepts and tooling covered in the Hello Nextflow and Nextflow for RNAseq beginner training.