Daniel Straub

Hi, thanks for the reference to MACSE. However, I do not understand how that tool could fit into the pipeline. We do not produce alignments. Could you elaborate?

Thanks for the reply! Here are 3 more questions: - Does that mean MACSE could be used to filter ASV sequences before taxonomic classification for sequences that are likely COI...

Thanks! Because I am as well limited in time and have at the moment no projects relating to protein-coding marker genes, I cannot justify investing time into adding MACSE currently....

Hi there, > a separate pipeline parameter setting phred to default (“Auto” ), 33 (“FastqQuality”) or 64 (“SFastqQuality”) that sounds like a good addition to me. However, test data (that...

If only forward reads are ok, isnt that also sufficient for implementing phred score flexibility? I would think so.

Hi @amakunin , real data would be much better, than we could use a small subset for continuous integration testing. Please update in case you are able to share data.

I had a more detailed look at the code. Previously `derepFastq` was removed, see https://github.com/nf-core/ampliseq/issues/348. I do not think to re-introduce `derepFastq` is a good idea for the general usage,...

Dear @amakunin , could you test the solution as described above? I would like to have that solved or abandoned.

Thanks! > Should I submit these data as a pull request in the test data repo https://github.com/nf-core/test-datasets/tree/ampliseq or maybe just post here? A PR would be great, but if thats...

Hi @amakunin , sorry for the late reply. Allocating some time to ampliseq during the hackathon. I tested the elembio est data with ```nextflow run d4straub/ampliseq -r add-param-for-phred-encoding -profile singularity...