Michael Hall

> I'm wondering if a solution might be to add a third provider: source and based on the accession download from the original provider (e.g. SRR from SRA, ERR from...

Were you ever able to get to the bottom of this @walaj?

I created [this script](https://github.com/mbhall88/NanoVarBench/blob/main/scripts/dupdemux.py) to demux a duplex basecalled BAM. Takes a summary file after demultiplexing simplex reads and your duplex called BAM. There’s some options for dealing with situations...

There’s no barcodes in the duplex bam. But that script uses the assignment from the sequencing summary file from the simplex basecalling to assign barcodes for the duplex reads. I...

No I generally basecall after the fact also. But you can create a summary file with https://github.com/nanoporetech/dorado?tab=readme-ov-file#sequencing-summary the demux command also has an —emit-summary option which will place a summary...

> We do have already our own conda channel 😉 > > https://anaconda.org/nanoporetech @cjw85 Would be great if you could add a recipe for pod5 to it :)

Yes, this is what I am doing at the moment. But as mentioned earlier in this thread there are advantages to having a recipe available for tools that rely on...

> Could you open the issues on your repository? Agreed, this would be very handy. I've also created a recipe on bioconda for pyvcf3 https://github.com/bioconda/bioconda-recipes/pull/34505

Indeed, a machine-readable output format would be fantastic. Even something like a CSV would be nice.

I have also run into this problem with f-strings in creating rules in a for loop. From memory, I think what happens is that the last (or first? Can't remember)...