dadaist2-taxonomy-binning

dadaist2-taxonomy-binning - 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-taxonomy-binning -i TABLE -o OUTDIR 

• -i, –input-table FILE

  Input OTU table, the normalized and with taxonomy column. The default name is OTUs_Table-norm-rel-tax.tab.

• -o, –output-outdir DIR

  Output directory.

Output files

• 0.Kingdom.all.tab

  Relative abundances a the Kingdom level

• 1.Phyla.all.tab

  Relative abundances a the Phylum level

• 2.Classes.all.tab

  Relative abundances a the Class level

• 3.Orders.all.tab

  Relative abundances a the Order level

• 4.Families.all.tab

  Relative abundances a the Family level

• 5.Genera.all.tab

  Relative abundances a the Genus level

• tax.summary.all.tab

  Summary table (all ranks)

• taxonomic-overview.pdf

  Stacked bar plots in PDF format

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.