This is a bash script that interleaves separated pair-ended FASTQ files. I works with awk internally.
chmod +x interleave_fastq
./interleave_fastq -h
This will give you:
interleave_fastq [-h] filename.1.fq[.gz] filename.2.fq[.gz]
It works with either compressed and uncompressed files.
If the input is compressed, the output will also will be. So try something like:
./interleave_fastq sample.1.fq.gz sample.2.fq.gz > sample.fq.gz