module load bio #to load all bio modules module load cio/cutadapt/1.6 #to load cutadapt alone
cutadapt version 1.6 Copyright (C) 2010-2014 Marcel Martin <firstname.lastname@example.org> cutadapt removes adapter sequences from high-throughput sequencing reads. Usage: cutadapt -a ADAPTER [options] [-o output.fastq] input.fastq Replace "ADAPTER" with the actual sequence of your 3' adapter. The sequence may contain 'N' wildcard characters. The reverse complement is *not* automatically searched. All reads from input.fastq will be written to output.fastq with the adapter sequence removed. Adapter matching is error-tolerant. Multiple adapter sequences can be given (use further -a options), but only the best-matching adapter will be removed. Input may also be in FASTA format. Compressed input and output is supported and auto-detected from the file name (.gz or .bz2). Use the file name '-' for standard input/output. Without the -o option, output is sent to standard output. Some other available features are: * Trimming of 5' adapters and "mixed" 5'/3' adapters * Trimming a fixed number of bases * Quality trimming * Trimming paired-end reads * Trimming colorspace reads * Filtering reads by various criteria See http://cutadapt.readthedocs.org/ for the full documentation. Use "cutadapt --help" to see all command-line options.
See the official website: [http:// ]