Scythe Testing

File and Operation Overview

• Makefile dispatches cleaning and run.sh
• run.sh is what runs other trimmers under a variety of parameters, for each of the simulated read files (with all replicates).
• analysis.R contains R methods for matching simulated reads and their trimmed corresponding reads (for all trimmers tested) and comparing their length.

Trimmers

run.sh is designed to use the most recent Scythe version; it references it in the directory above the testing directory. Other trimmers must be in the $PATH environmental variable.

Trimmer Versions

• btrim, not versioned but the 2011-09-16 version of btrim_mac was downloaded from http://graphics.med.yale.edu/trim/. The Linux version btrim32 is also not versioned, but the 2011-02-31 version was used.
• cutadapt, version 1.0 was tested. This version is dated 2011-11-04 and downloaded from http://code.google.com/p/cutadapt/downloads/list.
• scythe version 0.981 was used.