Meaning of the default NSTI value of 2 in Picrust2

[Jess Palmer]

Hello,

In PICRUSt1, the default nearest sequence taxon index (NSTI) is set at 0.03 which was confirmed that it meant 97% similarity (so species level). However, in PICRUSt2, the default is set at 2 but I can’t find in the paper what that actually means… I need to confirm what is meant when my OTUs are matched with a ‘close relative’ so was hoping that the NSTI value correlated with a % similarity as with PICRUSt1. I see from past answers that the default NSTI is lenient but it would be great if I could have a more precise definition of what it means if possible!

Thank you in advance,

Jess 

[Gavin Douglas]

Hi there,

 

The NSTI and sequence similarity values are closely linked, but not perfectly. It does definitely correlate with % similarity overall. When you say that the cut-off for PICRUSt1 was 0.03, do you mean the recommended level for the weighted NSTI? That’s the abundance-weighted average NSTI value of all OTUs per sample, so it’s a little different to interpret as well (i.e., the most abundant OTUs could have low NSTI values, but there could still be many rare ones above 0.03). 

  

The NSTI refers to the distance in the tree to the nearest reference genome. So a NSTI value of 2 is quite high and is really just meant to filter out junk sequences.

You could lower it to something like 0.03 if you wanted to make the predictions were only based on 16S sequences that were very close to reference genomes.

Does that help?

Thanks,

Gavin

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