Hi @vheidrich,
Thanks for reaching out, these are great questions! I'll discuss below the differences between trimming and truncating (as they are utilized within the QIIME 2 core framework).
Trimming: The number of base pairs that will be removed from either the 3' or the 5' end. In QIIME 2, you'll most commonly see trim-left (which will trim off the requested number of base pairs from the 5' end), but in qiime feature-classifier extract-reads, there is also a trim-right parameter, which refers to the 3' end.
Truncating: The position at which reads will be truncated (counting from the 5' end). Reads that are shorter than the value provided will be discarded. The command you'll see this action represented by within QIIME 2 is trunc-len. Something to note is that in the denoising pipelines within the QIIME 2 core framework, truncation occurs before trimming.
Here is an example that may help further clarify - take the following words as sequence examples:
QIIME2
TRIMMING
TRUNCATION
I will first truncate the above sequences with this command:
trunc-len 7
This is what I will be left with:
TRIMMIN
TRUNCAT
Note that QIIME2 was dropped because it is shorter than the truncation of 7 that was specified.
I will now trim the remaining sequences with this command:
trim-left 2
This is what I will be left with:
IMMIN
UNCAT
Hope this helps!
Cheers :qiime2: 