Reproducible Scalable Pipeline For Amplicon-based Metagenomics (RSP4ABM)

RSP4ABM is a bioinformatic pipeline designed for convenient, reproducible and scalable amplicon-based metagenomics. RSP4ABM 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 “all in one” execution of all required 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. RST4ABM is capable of processing local sequencing reads as well as reads from the Sequence Reads Archive (SRA).

A complementary workflows enables preprocessing of reference taxonomic databases needed to classify taxa to amplicon sequences. Another workflow allows to predict in silico the expected taxonomic classification from selected reference genomes.

Note that RSP4ABM is a compilation of numbers 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 RSP4ABM.

• 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
• In silico validation tool
  • Title2
• Frequently asked questions (FAQ)
• In silico validation tool
  • Aim
  • Working principle
  • Requirements
  • Inputs
  • Execution