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Welcome to the YAMP wiki.

Briefly, YAMP (Yet Another Metagenomic Pipeline) aims at automating the analysis of metagenomic data. It has a strong focus on quality control, and allows the data processing from raw sequencing data up to functional annotation. More information can be found in the The YAMP workflow page, or the project GitHub README.

Please, before running YAMP, check if you have all the dependencies installed, as explained in the Getting started section.

This wiki includes several tutorials, but it is recommended to start with the How to run YAMP, which explains how to set YAMP parameters, and describes the files that will be produced in output -- you can read more about YAMP logs at this page. If you are in a hurry, you can have a look at the TL;DR instructions!

If you are using an HPC facility, please refer to the How to run YAMP on a HPC tutorial, and if you want to take advantage of a personalised config file, please read the How to use Nextflow profiles tutorial.

For specific usage scenarios, please refer to our tutorials about Single- vs paired-end reads, and How to run YAMP with QC'ed reads.

YAMP is designed to be used with container technology, and you can read more about this in the How to use Docker, and the How to use Singularity tutorial, or in the Multi image scenario page.