Dadaist2: highway to R

:package: See the repository

release version Conda Build Status Dadaist-CI

Standalone wrapper for DADA2 package, to quickly generate a feature table and a set of representative sequences from a folder with Paired End Illumina reads. Dadaist2 is designed to simplify the stream of data from the read processing to the statistical analysis and plots.

Dadaist2 is a highway to downstream analyses:

  • Generation of a PhyloSeq object, for immediate usage in R
  • Possibility to run in the pipeline a custom R script that starts from the PhyloSeq object
  • Generation of MicrobiomeAnalyst-compatible files. MicrobiomeAnalyst provides a web-interface to performgi a broad range of visualizations and analyses.
  • Generation of Rhea-compatible files. Rhea is a standardized set of scripts "designed to help easy implementation by users".

In addition to this, Dadaist:

  • Can automatically detect quality boundaries or trim the primers
  • Has a custom mode for variable length amplicons (i.e. ITS), to detect features longer than the sum of the paired-end reads.
  • Ships an open source implementation of UNCROSS2 by Robert Edgar.
  • Has a modular design that allows recycling parts of it in custom workflows.
  • Prepares a MultiQC-enabled overview of the experiment
  • Produces an easy to inspect HTML execution log

You can read more about the features.

The workflow