Introduction

Tau-typing is a bioinformatics analysis pipeline tuned for identifying genes or genomic segments which most closely reflect the genome-wide phylogenetic signal of a given organism using the rank correlation statistics (Kendall's tau or Spearman's rho).

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The Nextflow DSL2 implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been installed from nf-core/modules.

Development and testing of this pipeline used singularity as the container technology and Sun Grid Engine (SGE) for testing on cluster environments.

Pipeline summary

1. Transfer annotations (Liftoff)
2. Extract features (GFFRead)
3. Compare genome sequences - ANI or Maximum Likelihood (FastANI, Phangorn)
4. Compute the core genomes (PIRATE)
5. Rank individual features against WGS (Custom (R) scripts)
6. Create sets of features from best-correlating features (Custom (Perl) scripts)
7. Rank sets against WGS (Custom (R) scripts)
8. Tabulate results (MultiQC)

Quick Start

1. Install Nextflow (>=21.10.3)

2. Install any of Docker, Singularity (you can follow this tutorial), Podman, Shifter or Charliecloud for full pipeline reproducibility (you can use Conda both to install Nextflow itself and also to manage software within pipelines. Please only use it within pipelines as a last resort; see docs).

3. Download the pipeline and test it on a minimal dataset with a single command:

   nextflow run hseabolt/tautyping -profile test,<YOURPROFILE> --outdir <OUTDIR>

   Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (YOURPROFILE in the example command above). You can chain multiple config profiles in a comma-separated string.

   • The pipeline comes with config profiles called docker, singularity, podman, shifter, charliecloud and conda which instruct the pipeline to use the named tool for software management. For example, -profile test,docker.
   • Please check nf-core/configs to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use -profile <institute> in your command. This will enable either docker or singularity and set the appropriate execution settings for your local compute environment.
   • If you are using singularity, please use the nf-core download command to download images first, before running the pipeline. Setting the NXF_SINGULARITY_CACHEDIR or singularity.cacheDir Nextflow options enables you to store and re-use the images from a central location for future pipeline runs.
   • If you are using conda, it is highly recommended to use the NXF_CONDA_CACHEDIR or conda.cacheDir settings to store the environments in a central location for future pipeline runs.

4. Start running your own analysis!

   nextflow run hseabolt/tautyping --input samplesheet.csv --outdir <OUTDIR> -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>

Documentation

The Tau-typing pipeline comes with documentation about the pipeline usage, parameters and output.

Credits

Tau-typing was originally written by hseabolt.

We thank the following people for their extensive assistance in the development of this pipeline:

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

Citations

If you use Tau-typing for your analysis, please cite it using the following citation:

Tau-typing: a Nextflow pipeline enabling on-demand, high-resolution molecular typing for pathogen genomics

Matthew H. Seabolt, Arun K. Boddapati, Joshua J. Forstedt, Kostantinos T. Konstantinidis.

Tau-typing: a Nextflow pipeline for finding the best phylogenetic markers in the genome for genomotyping of microbial species

To be submitted to Bioinformatics

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

You can cite the nf-core publication as follows:

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.