/usr/bin/fastq-interleave is in last-align 712-1ubuntu1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 | #! /bin/bash
test $# = 2 || {
cat <<EOF
Usage: $0 x.fastq y.fastq
Read 2 fastq files, and write them interleaved.
Assumes 1 fastq per 4 lines, i.e. no line wrapping.
EOF
exit
}
paste <(cat "$1" | paste - - - -) <(cat "$2" | paste - - - -) | tr '\t' '\n'
# Is this better?
#paste <(zcat -f "$1"|paste - - - -) <(zcat -f "$2"|paste - - - -)|tr '\t' '\n'
# This does not interpret "-" as stdin:
#paste <(paste - - - - < "$1") <(paste - - - - < "$2") | tr '\t' '\n'
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