Man page - fastq-join(1)

Packages contains this manual

Package:  ea-utils
apt-get install ea-utils

Manuals in package:
• fastq-clipper(1)
• fastq-stats(1)
• fastq-multx(1)
• varcall(1)
• fastx-graph(1)
• determine-phred(1)
• fastq-join(1)
• fastq-mcf(1)
• sam-stats(1)
• ea-alc(1)
Documentations in package:
• ea-utils

Manual

FASTQ-JOIN

NAME
SYNOPSIS
DESCRIPTION
OPTIONS

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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.

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