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

[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!