dadaist2-alpha

dadaist2-normalize - Normalize OTU table using the Rhea protocol. The Rhea protocol (https://lagkouvardos.github.io/Rhea/) is a complete set of scripts to analyse microbiome files.

This wrapper is part of the AutoRhea script bundled with Dadaist2. If used, please, cite the Rhea paper (see below).

Authors

Andrea Telatin and Rebecca Ansorge

Usage

dadaist2-normalize [options] -i TABLE -o OUTDIR 

• -i, –input-table FILE

  Input file, the normalized OTU table

• -o, –output-outdir DIR

  Output directory

• -e, –effective-richness FLOAT

  Effective richness (default: 0.0025)

• -s, –standard-richness INT

  Standard richness (default: 1000)

Output files

• alpha-diversity.tab

  Table with: Richness, Shannon.Index, Shannon.Effective, Simpson.Index, Simpson.Effective, and Evenness for each sample

Citation

If you use Rhea in your work please cite/attribute the original publication:

 Lagkouvardos I, Fischer S, Kumar N, Clavel T. (2017) 
 Rhea: a transparent and modular R pipeline for microbial profiling based on 16S rRNA gene amplicons. 
 PeerJ 5:e2836 https://doi.org/10.7717/peerj.2836

Source code and documentation

This wrapper is part of Dadaist2 freely available at https://quadram-institute-bioscience.github.io/dadaist2 released under the MIT licence. The website contains further DOCUMENTATION.