How many tables can you merge in one command of feature table merge?

[Jen_S]

Hello All,
We have 23 sequencing runs that we need to denoise separately using dada2 and would like to merge together after denoising. Can we use feature-table-merge in qiime2 to merge them all together at once with one command? i.e. one merge command for all 23 denoised .qza files.
or
Does feature table merge require two tables at a time and then successive merging for all additional tables?

I saw this post merging
but in 2017 it looks like this was not solved. Has it been solved now?

Side note: I could not find the documentation on feature-table-merge in qiime2.

Thank you so much!
Jen

[Nicholas_Bokulich]

@Jen_S

Can we use feature-table-merge in qiime2 to merge them all together at once with one command?

Oh yeah, you can merge as many tables as you like! Like this:

qiime feature-table merge \
    --i-tables table1.qza \
    --i-tables table2.qza \
    --i-tables table3.qza \
    --i-tables table4.qza \
    --o-merged-table merged-table.qza

@Jen_S

but in 2017 it looks like this was not solved.

This has in fact been solved since 2017 — see the end of the topic you linked to:

Merging many feature tables

QIIME 2 2017.12 is now out, and has the ability to merge many tables at once (among other things)!

@Jen_S

Side note: I could not find the documentation on feature-table-merge in qiime2.

You can use --help to read the manual on any CLI command... or here are the docs you are looking for:
https://docs.qiime2.org/2019.10/plugins/available/feature-table/merge/
See also a tutorial example:
https://docs.qiime2.org/2019.10/tutorials/fmt/#merging-denoised-data

Good luck!

[Jen_S]

Thank you so much for this!
Appreciate the speedy response!
jen