---
name: "fastq-interleave"
section: "1"
platform: "linux"
package: "last-align"
version: "1609-1+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/fastq-interleave"
---

# fastq-interleave(1)

Read 2 fastq files, and write them interleaved

## NAME

fastq-interleave - Read 2 fastq files, and write them interleaved

## SYNOPSIS

**fastq-interleave** *x.fastq y.fastq*\
 **fastq-interleave** *x.fastq.gz y.fastq.gz*

## DESCRIPTION

Read 2 fastq files, and write them interleaved.  Keep just the first word of header lines, and append "/1" and "/2" if they are otherwise identical.  Assumes 1 fastq per 4 lines, i.e. no line wrapping.