File and Operation Overview
Makefiledispatches cleaning and
run.shis what runs other trimmers under a variety of parameters, for each of the simulated read files (with all replicates).
analysis.Rcontains R methods for matching simulated reads and their trimmed corresponding reads (for all trimmers tested) and comparing their length.
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.
- btrim, not versioned but the 2011-09-16 version of
btrim_macwas downloaded from http://graphics.med.yale.edu/trim/. The Linux version
btrim32is 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.