Alignment on Reference Database

[TurboQiimer]

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

[colinbrislawn (Colin J Brislawn)]

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

[TurboQiimer]

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:

Q2-alignment: reference based alignment using SINA

This is a draft Community Tutorial. The command qiime alignment sina may not yet be available in your installation of Qiime2 Comments and suggestions would be greatly appreciateed Aligning sequences to match a reference alignment Background Traditional, de novo methods mututally align a set of unaligned sequences to create a multiple sequence alignment (MSA) from scratch. Re-running these methods with additional sequences will create MSAs with varying numbers of…

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?

[colinbrislawn (Colin J Brislawn)]

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.

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

@TurboQiimer

I do not need to draw a phylogeny tree.

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