This is the command fastq-join that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
fastq-join - ea-utils: join two paired-end reads on the overlapping ends
fastq-join [options] <read1.fq> <read2.fq> [mate.fq] -o <read.%.fq>
fastq-join: invalid option -- 'h' Unknown option `-h'.
Joins two paired-end reads on the overlapping ends.
-o FIL See 'Output' below -v C Verifies that the 2 files probe id's match up to
use ' ' (space) for Illumina reads
-p N N-percent maximum difference (8) -m N N-minimum overlap (6) -r FIL
Verbose stitch length report -R No reverse complement -x Allow insert <
You can supply 3 -o arguments, for un1, un2, join files, or one
argument as a file name template. The suffix 'un1, un2, or join' is appended to the file,
or they replace a %-character if present.
If a 'mate' input file is present (barcode read), then the files
'un3' and 'join2' are also created.
Use fastq-join online using onworks.net services