tutorial for merging different sequencing data in qiime2

[saif_s (saif)]

Hi everyone,

I have 4 years of sequencing data, 3 years are sequenced together (same seq batch), and one year sequenced separately. Is there a tutorial that walks through how to process and merge those sequencing data?

Thank you

[SoilRotifer (Mike Robeson)]

Hi @saif_s ,

All you need to do, once you've processed the runs separately you can merge the feature-tables, sequence files, and taxonomy files using these commands:

• feature-table merge
• feature-table merge-seqs
• feature-table merge-taxa

You can read more about the various plugin commands here.

-Cheers!
-Mike

[saif_s (saif)]

Thank you Mike! Do you happen to have a tutorial on how to process them in qiime2? like what are the steps and commands that I can follow to process the data to get to the merging step?

[SoilRotifer (Mike Robeson)]

Everything is available through the various tutorials:

• Using QIIME 2
• QIIME 2 Cancer Microbiome Intervention Tutorial
• Other QIIME 2 Tutorials
• QIIME 2 YouTube Channel Workshop Playlists

-Mike

[saif_s (saif)]

I really appreciate all the help you provided Mike! Thank you so much.

[gregcaporaso]

One more specific reference to add to @SoilRotifer's list: this tutorial specifically shows what this workflow might look like. A new version of it will be available with the new version of the QIIME 2 amplicon distribution documentation, coming with the 2025.4 release.