A minimal wrapper for running cutadapt (http://cutadapt.readthedocs.io/en/stable/) in batch mode. Made for the Monckton Group at University of Glasgow, so there may be specific behaviour in this program for the way in which we label our MiSeq data. I honestly can't remember.

Install

python setup.py install
or
pip install batchadapt

Usage

Example usage:

$ batchadapt [-h/--help] [-v] [-i INPUT] [-o OUTPUT] [-fwfp AAAAA] [-rvfp GGGGG] [-e 0] [-ov 10]

Arguments

Run batchadapt with the '--help' argument for detailed explanations of what each argument does.