eemisdada2

Packaging of dada2 for EEMiS, and other, users.

DADA2 is an error correction algorithm for Illumina amplicon reads. This repository offers four R scripts that lets you run the four main steps (cleaning and merging is performed by the same script) in the processing separately, saving intermediate results:

1. dada2filter: quality and length trimming
2. dada2errmodels: calculation of error models from the data
3. dada2cleanNmerge: sequence correction and merge
4. dada2bimeras: filter bimeras, create final tables

Requirements

DADA2 can be installed from the Bioconductor site.

DADA2 requires headers for the libcurl4-gnutls library. In Debian they can be installed with this command:

$ sudo apt install libcurl4-gnutls-dev

The Bioconductor package DECIPHER is also required.

Installation

The scripts in this repository are easiest to install by cloning the repo and creating symlinks to the actual scripts in src/R.

Assuming you have $HOME/bin in your PATH variable and a dev directory in your home directory where you keep repositories like this, you would:

$ cd ~/dev/
$ git clone https://github.com/erikrikarddaniel/eemisdada2.git
$ cd ~/bin
$ ln -s ~/dev/eemisdada2/src/R/*
$ cd ~
$ dada2filter --version

(The last command just checks that everything is working.)

Now, you're ready to run the scripts, in the order specified above, from any directory. All scripts have a --help flag as documentation.

Automation via Make

In my biomakefiles repository, there's a makefile-based workflow implementation with documentation.