Daniel Straub

Yes, there could be a way of having Nanopore reads fastq files without Illumina data as input. And that would be desirable in this pipeline. But it would be important...

Hi there, unfortunately I cannot really troubleshoot without the complete error message. Could you please post the error message and/or the nextflow log of that run? I assume what you...

> MEGAHIT-NS.1754.004.IDT_i7_93---IDT_i5_93.CZS48M.6.fa_busco.log.txt > MEGAHIT-NS.1754.004.IDT_i7_93---IDT_i5_93.CZS48M.6.fa_busco.err.txt > MEGAHIT-NS.1754.004.IDT_i7_93---IDT_i5_93.CZS48M.6.fa_busco.failed_bin.txt Those show that BUSCO fails occasionally to find any marker genes. Thats is not nice, but expected in some cases when MAGs/bins are small...

Unfortunately I cannot pinpoint the problem. Maybe @skrakau can find the cause here (but she is currently unavailable, keeping this here as reference fore later). Your best shot for now...

> Given that positive Barrnap predictions for different domains (e.g. rrna.arc, rrna.bac, rrna.euk) are non-mutually exclusive, it would be good if SBDI output could reflect some evaluation of e-values for...

This seems bad. Could you additionally try using [--busco_reference](https://nf-co.re/mag/2.2.1/parameters#busco_reference) or [--busco_download_path](https://nf-co.re/mag/2.2.1/parameters#busco_download_path). That would mean having the files locally and therefore omitting any downloading step.

Also, please do not use `-r fix-convert-depths-gzip` but `-r 2.2.1` ;)

This might be a helpful feature. As far as I know there is work ongoing for wrapping DADA2 directely in this pipeline instead of QIIME2 using DADA2. Therefore I am...

@DiegoBrambilla is planning to implement dada2 for PacBio analysis and could immediately add that demultiplexing step :)

Demultiplexing could be done via cutadapt as documented [here](https://cutadapt.readthedocs.io/en/stable/guide.html#demultiplexing). I never come across the need for demultiplexing in the pipeline, but if anyone does, please mention it here and I...