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Makefile
README.md
analysis.R
btrim_adapters.fa
generate-reads.R
read-sim.R
reads.fastq
run.sh

README.md

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

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