---
name: "fastq-join"
section: "1"
platform: "linux"
package: "ea-utils"
version: "1.1.2+dfsg-9+b3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/fastq-join"
---

# fastq-join(1)

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

## 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.