NAME

       fastq-join - ea-utils: join two paired-end reads on the overlapping ends

SYNOPSIS

       fastq-join [options] <read1.fq> <read2.fq> [mate.fq] -o <read.%.fq>

DESCRIPTION

       fastq-join: invalid option -- 'h' Unknown option `-h'.

       Joins two paired-end reads on the overlapping ends.

OPTIONS

       -o  FIL     See 'Output' below -v C       Verifies that the 2 files probe id's match up to
       char C

              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 <
       read length

       Output:

              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.