So i have a question regarding basecalling with Dorado. Say i start with a POD5 file from a sequencing run and I now want to basecall it with a sup model I already have downloaded, demultiplex and trimm all adapters and barcodes.

I find it somewhat difficult to make out from the documentation if you would need to run 2-3 seperate Dorado commands (Dorado basecall and Dorado demux, potentially with a third one for trimming?), or if you could do it all in one command. Because if I look at the most recent documentation, especially regarding the trimming (see link below at the bottom), I would read it as "If you would run demux seperately, do not trim in basecalling". But would this then also not imply that in a single Dorado command, you could perform basecalling, demux and trimming like the command in the "Effect on demultiplexing" section:

dorado basecaller <model> reads/ --kit-name <kit-name> --trim all --emit-fastq --output-dir dir1

https://software-docs.nanoporetech.com/dorado/latest/basecaller/read_trimming/

Would the above command for example result in trimmed, demultiplexed reads in fastq format, with a file per barcode?

Any input from more experienced users is greatly appreciated!