Alignment on Reference Database

SINA alignment action/method does not exist in Qiime2. Could you please introduce another way to do that in Qiime2?

The qiime 2 plugin fragment-insertion can be used to make trees:
https://library.qiime2.org/plugins/q2-fragment-insertion/16/

Is this what you wanted to do with SINA?

Colin

Let me give you an example. I was reading a paper written ‘Sequences shorter than 300 nucleotides orlonger than 600 nucleotides were also discarded. The unique se-quences were then aligned in mothur by default setting with referring to the pre-aligned mcr Asequences provided by the Fun-gene Pipeline database’.

I do not need to draw a phylogeny tree. I want only align my sequences with a reference sequences. I found this message in Qiime2 forum:

I am looking for a plugin/action/ method or tool in Qiime2 to align my sequences (query) with reference sequences. By the way, there is an alignemt option in Qiime2, Maff, but its function is de-novo. it does not align the query on the reference sequences.

https://docs.qiime2.org/2019.4/plugins/available/alignment/mafft/

Now, can you help me with this details I gave to you?

Yes, thank you for providing me with those details.

The method you cited mentions mothur:

unique se-quences were then aligned in mothur

mothur uses a reference msa when building feature, and some Qiime 2 plugins like dada2 do not need a reference at all.

If you want to use SINA, that community tutorial is a good place to start. MAFFT now supports ref based alignments, but those features are not available in the Qiime 2 plugin yet.


I have another question for you, if you are interested in answering.

The only time I do MSA is when want a phylogeny tree for UniFrac distances or graphs. Why do you want to do MSA?

Colin

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.