joining non-overlaping paired reads

[splaisan]

Hi all,

I am looking for a fast executable that can join read pairs into single pseudo-reads so that I can apply FastQC on the joined sequences instead of performing two independent fastQC runs.
I wonder why fastQC does not offer that option out of the box!!

I could make my own simple perl/python/java code (using chat-gpt) but am sure there is a more performant compiled version somewhere (my best score is ~6sec / million PE150).

Note: the reads are considered non-overlapping, although many likely are, because I want to get the quality check of the full raw read pair.
I do not intend to merge them for further analysis as they would not correspond to real sequences anymore (plenty of tools for merging exist but will force merging).

Any advice is welcome
Cordially
Stephane