Markus Schlegel

Thanks for the pull request. I apologize for not yet looking at this. The reason is that, even though I agree that this is a good idea, I would prefer...

I can confirm this issue. Looking at the logfile, it appears more of a problem with de-replication, which is independent of whether VSEARCH or USEARCH are used for denoising. ```...

This command will replace the problematic code as a workaround: ```bash sed -i "s/--derep_fulllength', filter_out, '--relabel', 'Read_', '--sizeout', '--output/--fastx_uniques', filter_out, '--relabel', 'Read_', '--sizeout', '--fastaout/g" "$CONDA_PREFIX/lib/python3.10/site-packages/amptk/unoise3.py" ```

According to the VSEARCH documentation, the only difference is that `--fastx_uniques` can handle FASTQ files (also output) and `--derep_fulllength` cannot. I think that this just follows the behaviour of USEARCH,...

Thanks a lot for pointing me at your implementation, it looks very interesting. In fact, I have also been working on a redesign of the parallel API with at least...

I finally had another look, although I still didn't have the opportunity to test and benchmark it by myself. But the approach looks elegant and it seems like a nice...

Although not exactly comparable, I hope this fits in here: We have been evaluating the use of ONT (MinION / R10.4) for ITS barcoding of fungal specimens (~pure extracts, *not*...