cd QTQ
chmod +x ./*.sh
./qc-trim-qc.sh
cd ~/Desktop
mkdir GenopicsApps
cd GenomicsApps
Download Fastp and Trimmomatic executables and keep inside GenomicsApps.
get http://opengene.org/fastp/fastp
chmod a+x ./fastp
or download specified version, i.e. fastp v0.23.4
wget http://opengene.org/fastp/fastp.0.23.4
mv fastp.0.23.4 fastp
chmod a+x ./fastp
Download Trimmomatic
wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.39.zip
unzip Trimmomatic-0.39.zip
rm Trimmomatic-0.39.zip
Run: I: Input path [String]
O: Output path [String]
L: Minimum length of reads to keep [Int]
T: fp (Fastp) or Tr (Trimmomatic)
./qc-trim-qc.sh -I /path_to_input_data_directory/ -O /path_to_Output_directory/ -L 35 -T fp