Take a pair of fastq.gz files and produce interleaved fastq output

interleave_gzipped_fastq.sh

#!/bin/bash

# This script can be usd to interleave paired fastq.gz files to produce interleaved fastq stdoutput.
# This is quite useful if you don't want to create temporary fastq files (i.e. trimmed.fastq.gz) to run aligners
# Use bash not sh

READ1=$1
READ2=$2

paste <(zcat $READ1 | paste - - - - ) <(zcat $READ2 | paste - - - - ) | tr '\t' '\n'