This is the work of:
Erik Aronesty (2013). TOBioiJ : "Comparison of Sequencing Utility Programs", DOI:10.2174/1875036201307010001
The Versioning here is awful. I've bumped the version with no alterations to the original algorithm of Erik.
git clone https://github.com/brwnj/fastq-multx cd fastq-multx make
Sequences are sometimes output to STDOUT in a different order on OS X versus Redhat, therefore some tests may fail.
fastq-multx -B barcodes.tsv -m 0 \ Undetermined_S0_L001_I1_001.fastq.gz \ Undetermined_S0_L001_R1_001.fastq.gz \ Undetermined_S0_L001_R2_001.fastq.gz \ -o n/a -o %_R1.fastq -o %_R2.fastq