Measuring representation in a fragment insertion tree

[hsapers (Haley Sapers)]

Following along on YouTube - thanks for the live stream

When evaluating how ‘good’ a reference alignment is for building a tree based on fragment insertion, is there a ‘quick and dirty’ way to see how many of your amplicons are represented in the ref set and over what length the represented amplicons align over?

thanks

[Nicholas_Bokulich]

Hi @hsapers,

@hsapers

When evaluating how ‘good’ a reference alignment is for building a tree based on fragment insertion

I can't think of a QIIME 2 method used for evaluating an existing alignment specifically...

however, I think I can answer this:

@hsapers

is there a ‘quick and dirty’ way to see how many of your amplicons are represented in the ref set and over what length the represented amplicons align over?

Yes! See q2-quality-control's evaluate seqs method. It uses BLAST under the hood to align query sequences against a reference set and report the quality of alignments (or lack thereof). That would be both quick and dirty, and give you a rough idea of how well your query sequences align to the reference (reporting coverage and % id etc).

This action even has an option to visualize the alignments but that's kind of clunky so I recommend the tabular results (no visualization) if you have a large number of sequences or long sequences.

I hope that helps!