add option to remove primers on trim-alignment

[danpal96]

version: apptainer docker://quay.io/qiime2/amplicon:2024.10

I am currently using the trim-alignment plugin to trim sequences obtained from processing nanopore data with amplicon_sorter and I would like to exclude the primers from the final sequence, but the current behavior is to keep them.

[mikerobeson]

Hi @danpal96, for the moment this is intended as outlined in the help documentation for this action. We'll look into changing that. :-)

We recently updated trim-alignment as it was not working as intended when extracting the amplicon region using the primers. You can pip install the current repo into your QIIME 2 environment to obtain the fix.

One current work around to exclude the primers from your alignment would be to: export the current alignment containing the primers, and open within an alignment viewer. Then record the base just after the forward primer 3' position and the base before reverse primer 5' position. Then supply those alignment positions directly using the --p-position-start and --p-position-end flags of rescript trim-alignment.

[danpal96]

Thanks for the response. What I ended up doing was something similar: I created "primers" from the 25 nucleotides downstream of the primers of a random sequence in the alignment. It is just a bit inconvenient.