Dadaist2 features
Fast track to R and numerical ecology
Dadaist is a simple and modular toolkit to streamline the generation of plots and analyses for microbiome studies, based on the popular DADA2 algorithm for reads denoising.
What makes Dadaist an interesting alternative to other suites is the focus on reproducible downstream analyses (thanks to the automatic generation of a PhyloSeq object and the preparation of files ready to be analysed with MicrobiomeAnalyst or Rhea)
- 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 perform 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".
- Generation of MultiQC ready report
Mitigation of Cross-talk noise
Using dadaist2-crosstalk it is possible to reduce the noise introduced by the spillover of reads from one sample to another sample in the same sequencing lane, using the UNCROSS2 algorithm.
Long targets workflow
A custom DADA2 workflow that does not rely on read merging to identify molecular species longer than the sequencing reads length. See some ITS notes.
Advanced logs and notifications
Dadaist2 is both a collection of tools (to create your own pipeline, for example using NextFlow) and a standalone pipeline designed to be easy to run from a local computer.
- Colored terminal output to follow the progress of the pipeline
- Optional notification popups to follow the progress of the major steps while doing something else
- Regular text logs are also collected in an easy to browse HTML report.