squigulator 4kHz vs 5kHz

Can this tool account for differences between the 4kHz and 5kHz sampling frequency (switchover after ONT sequencing software version 23.04)?

Mar 12 '24 12:03 awgymer

Yes. The latest squigulator v0.3.0 with the -x dna-r10-min and -x dna-r10-prom profiles generate 5KHz data by default. If you want old 4KHz data, specify -f 4000 along with -x dna-r10-min or -x dna-r10-prom. Hope it is clear enough?

Mar 12 '24 18:03 hasindu2008

Ideal, thank you!

Mar 12 '24 23:03 awgymer

Sorry I am now looking at running this and I realise I'm not sure I fully understand the logic behind -f 4000?

This simply sets the coverage depth to 4000 I thought? I'm not sure how this would relate to the data sampling frequency of 4 vs 5 kHz.

Perhaps I have to just use two versions of squigulator to get r10 data at both 4k and 5k sample rate?

Mar 14 '24 13:03 awgymer

Oh my bad. I told you the wrong option. You should be using --sample-rate not -f. Sorry about the inconvenience.

Mar 14 '24 22:03 hasindu2008

No worries, thanks for the clarification

Mar 14 '24 22:03 awgymer