Analysis of 16S data from different regions using q2-fragment-insertion or other substitution

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Hi everyone,

I am a beginner in 16S data analysis. I've read lots of discussions about analyzing 16S data from different regions in this forum and found that

  • merging table after taxonomic classification,

  • trimming reads to same region before DADA2,

  • using q2-fragment-insertion

are recommanded. At first, I was about to use q2-fragment-insertion, but then I found it will be no longer supported in 2025.10. I also found q2-kmerizer is recommanded, so here is my questions:

  1. Can q2-kmerizer merge 16S data from different regions for taxonomic analysis?
  2. Is there any other substitution can be used?

Thank you all,
Julio

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Hi @Julio ,
Another option for merging data from multiple regions would be closed-reference OTU clustering.

This is still an option. It will still be present and totally valid in the 2025.7 release. It will only be dropped in 2025.10. But you can switch between environments to use the different distribution versions, so it's not like fragment insertion is no longer available.

No. kmerizer provides a similar approach for pseudo-phylogenetic diversity estimates, but not when comparing data from different regions, as the kmer profiles would be different.

I suggest just installing the 2025.7 distribution once it is available and keep this around for running fragment-insertion, otherwise closed-reference OTU clustering would be the most similar alternative that will remain available in future releases of the amplicon distribution.

Good luck!

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Thanks for your immediate response! I will also try closed-reference OTU clustering and compare the results with those using q2-fragment-insertion.

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