Combining split_on_adapter with duplex calling

[Coryza]

Hi,

From your readme.md it's unclear for me if / how to one can combine the split_on_adapter tool with the guppy duplex calling? The output files of the first do not match with the input files of the second - and I see no parameter in the guppy duplex basecaller to indicate that potentially reads have been split.

Thanks,

Koen

[Rasinj]

Hi @Coryza, you would be better off relying on the read splitting that is already integrated in guppy, it works in a similar fashion to split_on_adapter and should make for a more seamless workflow as well. There is a --do_read_splitting option that you can give to guppy_basecaller (and to guppy_basecaller_duplex). I would also suggest setting the --min_score_read_splitting to 58 if doing this.

[Coryza]

Hi,

Thanks for the quick response. Would it be possible to give guppy custom adapters (if not directly, could one edit something hard coded). This is for example possible with the split_on_adapter. Also, how would that work when providing read pairs as a txt for these 'chimeric reads'? Just the read versus itself?

Much appreciated, Koen

On Wed, Aug 10, 2022, 09:54 o @.***> wrote:

Hi @Coryza https://github.com/Coryza, you would be better off relying on the read splitting that is already integrated in guppy, it works in a similar fashion to split_on_adapter and should make for a more seamless workflow as well. There is a --do_read_splitting option that you can give to guppy_basecaller (and to guppy_basecaller_duplex). I would also suggest setting the --min_score_read_splitting to 58 if doing this.

— Reply to this email directly, view it on GitHub https://github.com/nanoporetech/duplex-tools/issues/17#issuecomment-1210299688, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABW4RWSUKYJTNAWUE44HDCTVYNN4RANCNFSM56DFTXMQ . You are receiving this because you were mentioned.Message ID: @.***>

[Rasinj]

Hi Koen,

Sorry for later reply this time. There is a .cfg file in the barcoding folder in guppy/data where you can change the mid-adapter. I would have to refer to someone else for the guppy questions unfortunately, possibly better asked on the community I think.

[callumparr]

Is duplex calling restricted to kit 12 chemistry and above? Judging by the guppy config files it seems this is the case.

[onordesjo]

@callumparr, I don't think there's any restriction to kit12 chemistry and above, but I shall ask around and check. It may not be supported, but that also may not stop it from being possible (:

[onordesjo]

@callumparr, people are responding that it should work in principle even if we don't support it. I wouldn't say there'd be any harm in trying if you happen to have some and see what happens!

[callumparr]

From alignments alone, I am seeing some potential. So updated guppy should output potential partners regardless of the config file used?

Also in general about the duplex. Is the length of the follow-on strand always similar?

I am seeing some alignments that overlap but on the opposite strands for the same read but often the alignment for the later portion of the read is shorter.