Difference between denoise-single and denoise-pyro in DADA2

Hey guys, I have raw sequence which had been sequenced on Ion Torrent machine. I had followed the pipeline provided for Ion-torrent sequences and I had also done with denoise-single command with same parameters mentioned in the pipeline. When I ran the command with denoise-pyro it took longer time and when I done with denoise-single it took some time, I have two questions
A) Why the denoise-pyro took longer time.?
B) When I compared both the results there was only an small change in the frequency so can we conclude that we can either commands…? (i.e can we use denoise-single with parameter p-trim-left 15 and use the representative sequences for further analysis)

I am new to Bioinfomatics analysis especially QIIME2

Hello @Sreevatshan,

Great question! While denoise-pyro and denoise-single both run on forward reads, they have different settings optimized for the error model of Ion Torrent vs Illumina.

For Illumina, the Q-score represents the chance of a point mutation, like ATT -> GTT.
For Ion Torrent, the Q-score represents the chance of an insertion or deletion, like ATT -> AAATT.

These different settings lead to different run times.

In the code, compare the settings used for denoise_single() and denoise_pyro().

Because you observe the results to be similar, that seems OK to me… But I can see reviewer #3 asking why you didn’t used denoise-pyro on your Ion Torrent reads. :grimacing: Probably safer to use the defaults, unless you have positive controls to show the methods are equally good! Do you have any positive controls on this run? :thinking:


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Hey @colinbrislawn Thank you so much for the reply, No,I don’t have an positive control, Infact I had downloaded the sequences from an study…! I think it’s safe to run with denoise-pyro then…!

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