fastq-join1
Ea-utils: join two paired-end reads on the overlapping ends
Usage
fastq-join [options]
<read1.fq>
<read2.fq>
[mate.fq]
-o
<read.%.fq>
Overview
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
-oarguments, 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.