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.