http://edwards.sdsu.edu/labsite/index.php/robert/399-sorting-fastq-files-by-their-sequence-identifiers
Alternatively,
Pesort – Paired-End Sorter
Pesort takes one or two input FASTA or FASTQ files containing paired end reads (or single reads) and sort them so that the read pairs occur in the same order. It also sorts out which reads that don’t have a pair and outputs them to a separate file.
Cited from http://microbiology.se/software/petkit/
Or,
https://www.biostars.org/p/12576/
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