# Scythe

Scythe is a very simple adapter trimmer.

Scythe uses a Naive Bayesian approach to classify contaminant substrings in sequence reads. It considers quality information, which can make it robust in picking out 3′-end adapters, which often include poor quality bases.

The Bayesian approach Scythe uses compares two likelihood models: the probability of seeing the matches in a sequence given contamination, and not given contamination. Given that the read is contaminated, the probability of seeing a certain number of matches and mismatches is a function of the quality of the sequence. Given the read is not contaminated (and is thus assumed to be random sequence), the probability of seeing a certain number of matches and mismatches is chance. The posterior is calculated across both these likelihood models, and the class (contaminated or not contaminated) with the maximum posterior probability is the class selected.

## Documentation

## Usage on Bridges

To see what other modules are needed, what commands are available and how to get additional help type

module help scythe

To see what versions of Scythe are available type

module avail scythe

To use Scythe, include a command like this in your batch script to load the Scythe module:

module load scythe

Be sure you also load any other modules needed, as listed by the `module help scythe`

command.