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 major changes or bug fixes to the original algorithm.
git clone https://github.com/brwnj/fastq-join cd fastq-join make
Some tests are failing when building on OS X versus Redhat 6.6. OS X gives "nan" while Redhat gives "-nan".
fastq-join -p 2 -m 200 test_R1.fastq test_R2.fastq -o test_%.fastq