Mate-Pair Reads

HI, I’m having problems dealing with mate-pair reads. I have shotgun reads Novaseq 6000 with Nextera Mate-Pair Reads. I have noted that several online metagenomic platforms either will not analyze the samples, I’m assuming that they are setup for Paired End Reads and not processing Mate-Paired Reads properly. Does this make sense???
So trying to use Galaxy to pre-process the raw data. I have seen reference to Nextera LMP Long Mate Pair, I assume this is what I’m dealing with.

From what I have read, NxTrim is the recommended program to trim Mate-Pair Reads, but this is not available on Galaxy as far as I know. Is there another program to properly trim the Mate-Paired reads???

Thank you

cutadapt should generally be able to handle the mate pair case though you need to be careful configuring it correctly for the purpose.
You might want to consult the cutadapt command line tool documentation on top of the help provided in the Galaxy tool interface and read through this old SEQanswers thread including that Illumina pdf linked to in the original question there.

In any case, you will want to inspect the output carefully, possibly also after mapping (if read mapping is one of the steps in your envisioned analysis).

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