vtamR is a revised, completed version of VTAM (Validation and Taxonomic Assignation of Metabarcoding Data) rewritten in R. It is a complete metabarcoding pipeline:

  • Sequence analyses from raw fastq files of amplicon sequences till Amplicon Sequence Variant (ASV) table of validated ASVs assigned to taxonomic groups.
  • Handles technical or biological replicates of the same sample.
  • Uses positive and negative control samples to fine tune the filtering and reduce false positive and false negative occurrences.
  • Can pool multiple data sets (results of earlier analyses)
  • Can pool results from overlapping markers

Novelties compared to VTAM:

  • As it is a series of R functions, vtamR is highly adaptable to include/exclude and order different steps of the analyses
  • Includes SWARM for denoising
  • Graphic options
  • Include functions to get statistics of each filtering steps (read and variant count etc.)
  • ASV clustering to mOTU
  • The notion of marker and run has been dropped to simplify the analyses

Installation

  • Installation of vtamR package
  • Installation of third party programs
  • TaxAsssign data base

Tutorial: vtamR pipeline

  • How to construct a full metabarcoding pipeline
  • Supplementary functions
  • I/O files and data frames
  • Glossary
  • Trouble shooting

From fastq to data frame

Quality filtering, merging, trimming demultiplexing, dereplication according to different fastq content.

  • One sample per fastq - no tag - no primer
  • One sample per fastq - primer - no tag
  • Several samples per fastq - tags - primers

Make mock_composition file

How to pick the expected sequences in mock samples from your own data (in case you do not know them in advance).