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ea-utils provides command-line tools for processing biological sequencing data using methods such as barcode demultiplexing, adapter trimming, etc. It was primarily written to support an Illumina based pipeline - but should work with any FASTQs.
To run this software interactively in a Linux environment run the commands:
module load ea-utils fastq-clipper or fastq-joinorfastq-mcforfastq-multx