Reproducible Scalable Pipeline For Amplicon-based Metagenomics (zAMP)

zAMP is a bioinformatic pipeline designed for convenient, reproducible and scalable amplicon-based metagenomics. zAMP is a compilation of command-line tools and R packages that processes next-generation sequencing (NGS) from amplicon-based metagenomics reads into taxonomic profiles. Scripts running these tools are embedded in a Snakemake pipeline for reproducible, scalable and easy “one-command-line” execution of all steps, from QC to basic plotting. Tools and packages are made available into Singularity containers and Conda environments for easy and reproducible management of dependencies. zAMP is capable of processing local sequencing reads or reads stored on the Sequence Reads Archive (SRA). Complementary workflows enables preprocessing of reference taxonomic databases as well as in silico prediction the taxonomic classification obtained from reference genomes.

Please note that zAMP is a compilation of a number of published tools. We would be very grateful that you acknowledge our work but also the contribution of the developers of these tools in your publications using zAMP.

• System requirements and setup
  • Short description
  • Detailed description
• Taxonomic reference database preprocessing
  • Rational:
  • Working principle:
  • Execution:
  • References:
• Pipeline execution
  • 1. Select a method to define sequencing read files as input
  • 2. Create a working directory
  • 3. Create a links directory (for Sample and OldSampleName column as input)
  • 4. Write a sample sheet (aka metadata table):
  • 5. Write a config file
  • 6. Make sure Snakemake is available
  • 7. Run the pipeline
• Under the hood
  • Snakemake, environments and containers
  • Input output definition
  • Logging and traceability
  • Sequencing reads QC
  • Denoising
  • Taxonomic assignment
  • Post-processing
  • Picrust2
  • References
• Frequently asked questions (FAQ)
• In silico validation tool
  • Aim
  • Working principle
  • Requirements
  • Inputs
  • Execution