Sickle

Usage: sickle <command> [options]

Command:
pe	paired-end sequence trimming
se	single-end sequence trimming

--help, display this help and exit
--version, output version information and exit
#example using sickle on SINGLE end illumina data
sickle se -f input_file.fastq -t illumina -o trimmed_output_file.fastq
#example using sickle on PAIRED end illumina data
sickle pe -f input_file1.fastq -r input_file2.fastq -t illumina \
-o trimmed_output_file1.fastq -p trimmed_output_file2.fastq