What it does

Merge two files which constitute a paired-end file into a single, interleaved, paired-end FASTA/Q file

# r1.fq
@test-6/1
AGCTTGACGC
+
?.HCF@C>>F

# r2.fq
@test-6/2
TGCGAAGACC
+
>2?A?A@@7?

will produce the following paired file:

@test-6/1
AGCTTGACGC
+
?.HCF@C>>F
@test-6/2
TGCGAAGACC
+
>2?A?A@@7?

While this may not have been an illuminating example, it is important to note that this tool will properly interleave data. For example if you have the ids:

@r-1/1
@r-2/1
@r-3/1
@r-4/1

and

@r-1/2
@r-2/2
@r-3/2
@r-4/2

These will be interleaved as

@r-1/1
@r-1/2
@r-2/1
@r-2/2
@r-3/1
@r-3/2
@r-4/1
@r-4/2

Attribution

This Galaxy tool relies on the seqtk toolkit from lh3/seqtk, developed by Heng Li at the Broad Institute