Dadaist2: highway to R
See the repository
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
Contents
- Installation
- Dadaist2 features
- Dadaist2: a first tutorial
- Other tutorials
- Advanced usage
- Development notes
-
Help pages
- dadaist2
- dadaist2-addTaxToFasta
- dadaist2-alpha
- dadaist2-assigntax
- dadaist2-dada2fasta
- dadaist2-exporter
- dadaist2-getdb
- dadaist2-getdb-legacy
- dadaist2-importq2
- dadaist2-metadata
- dadaist2-normalize
- dadaist2-phyloseqCheck
- dadaist2-mqc-report
- dadaist2-phyloseqMake
- dadaist2-phyloseqMake-legacy
- dadaist2-taxonomy-binning
- dadaist2-taxplot
- dadaist2-crosstalk
- dadaist2-mergeseqs
- dadaist2-checkstats
- dadaist2-rundada