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 of vtamR package
- Installation of third party programs
- TaxAsssign data base
- How to construct a full metabarcoding pipeline
- Supplementary functions
- I/O files and data frames
- Glossary
- Trouble shooting
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
How to pick the expected sequences in mock samples from your own data (in case you do not know them in advance).