[!WARNING]

Project End-of-Life Notice

Metaphor is no longer under active development or maintenance. The code in this project was developed and maintained by a single individual, and the rapid pace of improvements in metagenomics methods makes it impractical to keep Metaphor aligned with current best practices. Going forward, I endorse and recommend the use of nf-core/mag, which is actively maintained by a broader community (including myself) and reflects up-to-date standards for metagenomic assembly and binning. The Metaphor manuscript remains a useful contribution, particularly in its evaluation of co-assembly versus individual-assembly strategies and the methodological insights it provides. However, the software itself should now be considered archived. Thank you to everyone who used, cited, or contributed to Metaphor 💜

Metaphor

A general-purpose workflow for genome-resolved metagenomics

[!IMPORTANT]
Citation – if you use Metaphor, please cite the Metaphor publication: Vinícius W Salazar et al. “Metaphor—A workflow for streamlined assembly and binning of metagenomes”, GigaScience, Volume 12, 2023, giad055, https://doi.org/10.1093/gigascience/giad055.

Metaphor is a Snakemake-based workflow for analysis of metagenomics short reads data. It includes the following steps:

• Quality control (with FastQC, fastp)
• Assembly (with Megahit, and evaluation is done with MetaQUAST)
• Read mapping (with Minimap2, Samtools)
• Binning (binners include Vamb, MetaBAT, CONCOCT; refinement is done with DAS Tool)
• Annotation (with Prodigal, Diamond, and the NCBI COG database)
• Postprocessing (with custom scripts)

Please cite these software if you use Metaphor. The bib files are located here for your convenience. Metaphor will support automatic citation in the future.

Metaphor aims to be concise, portable, and sustainable. It only includes third-party software that is properly packaged and easily installable. If you have any questions regarding Metaphor, please don’t hesitate to open an issue.

Check out our documentation!

Installation

The first thing that you need to install Metaphor is conda. To install it, please follow their user guide.

Once you have conda, we highly recommend that you use mamba for installing Metaphor. If mamba is not available, replace all mamba commands for conda.

To install, either create a new environment or install it in your preferred environment:

$ mamba create -n metaphor metaphor -c conda-forge -c bioconda
$ conda activate metaphor

You should see the (metaphor) indicator next to your prompt.

Testing

After installing, check if your Metaphor installation works:

# Check that the `metaphor` command works
$ metaphor -h

# You can see available options for testing Metaphor with:
$ metaphor test -h

# To test Metaphor (follow the screen prompts)
$ metaphor test

Testing may take a long time (a couple of hours), so please be patient. After testing, most dependencies will already be installed, which will save time on your next execution.

Usage

To run Metaphor on your data, we recommend that you create a configuration profile specific to your needs, and then create a tabular file containing your sample names and file paths. You can do this with the following commands:

# Create your configuration profile
$ metaphor config settings

# Create your tabular file with samples
$ metaphor config input -i <DIRECTORY_WITH_FASTQ_FILES>

# Then, to execute simply type 
$ metaphor execute

Metaphor will automatically detect the metaphor_settings.yaml and samples.csv files.

If you receive any errors, feel free to open an issue describing your problem.

DISCLAIMER

Metaphor is a derivative work of MetaGenePipe, originally released under the Apache 2.0 license, developed by Bobbie Shaban, Mar Quiroga, Robert Turnbull and Edoardo Tescari at Melbourne Data Analytics Platform (MDAP) at the University of Melbourne. MetaGenePipe is in press at The Journal of Open Source Software. For more information, please see the license file.