- A versatile and customizable workflow, from fastq treatment to statistical analysis.
- Integrating contaminant filtering based on control samples with decontam R package.
- Taxonomic assignment based on IDTAXA, and the abilitie to merge annotation from two databases, with validation step to keep the best assignment.
- Alpha and beta diversity indexes are compared between conditions with integrated statistical analysis (ANOVA, permanova and non-parametric test).
- Three main differential analysis methods (DESeq2, Metacoder, metagenomeSeq) are integrated to decipher differences between communities composition.
rANOMALY is full described in the publication:
Sebastien Theil and Etienne Rifa. « RANOMALY: AmplicoN WOrkflow for Microbial Community AnaLYsis ». F1000Research 10 (07/01/2021): 7. https://doi.org/10.12688/f1000research.27268.1.
A fully documented use case is available HERE
Datasets to reproduce the use case are available at this link
We share all the databases we currently use for IDTAXA in this link.