Data import ASV table with taxonomy and representative sequences

User Support
#1

Hello,
I have full length 16S+18S microbiome sequencing data (the read lengths of the sequences are not same). The data that I received is already demultiplexed, ASVs created and taxonomy assigned to the ASVs. I dont know which software was used to generate ASVs. I understand that I can import ASVs table and representative sequences into Qiime. I don't know what format the data should be in. I would like to import ASVs table and representative sequences and taxonomy into Qiime for further analysis (create alpha and beta diversity plots based on metadata). The format of data that I have is shown below.

  1. ASV table with taxonomy
    In this screenshot, I am showing 4 columns for samples, I have 96 such columns in each ASV table

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    image2000×748 689 KB

  2. Represetative sequences in fasta file

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    image1029×1047 375 KB

Also, I would like to know if it is possible to combine 10 such ASV table / representative fasta file pairs as shown above. I have 960 samples, the samples were processed in 10*96 well plates, each plate had its own barcode. I received the data as 10 ASV / representative file pairs, but they are essentially all a single data set. Is it possible to import and analyze all of them together? How do I import the metadata file in such a case.

Many thanks for any help or tips,
Gaurav

#2

Hi @Gaurav_C ,
It looks like your feature table is a tab-separated text file, but the format is very strange because each taxonomic rank is a separate column and you have uneven taxonomic ranks.

This cannot be imported as it is in a very unusual format.

First you should convert to a biom-format table (see the biom-format documentation online for more details; this software is not part of QIIME 2 but is installed as part of the QIIME 2 installation).

Once you have this in biom-format you can import to QIIME 2 as described in this tutorial:
https://docs.qiime2.org/2021.11/tutorials/importing/

The fasta file can be imported as-is — see also the tutorial above.

See the q2-feature-table plugin help documentation... that plugin has actions for merging feature tables (ASV tables) as well as sequence data. You can see the help docs for individual plugins here:
https://docs.qiime2.org/2021.11/plugins/

Sample metadata are not imported, they are just input directly as a TSV (in an appropriate format). See the tutorials at the documentation that I linked to to see some examples.

If you have any additional questions please open a separate topic to keep separate questions organized. Thanks!

good luck!