Justin Chu

I wouldn't worry about the warning. It just means redundant k-mers are collapsed and the filter becomes more sparse with a lower FPR. It doesn't really cause issues other than...

What do you mean by k-mer fasta? At any rate BBT needs redundant hits to confidentiality classify, the intent is to use raw fasta I would expect.

Were the genomes of [viral.kc.fasta.gz](http://opengene.org/viral.kc.fasta.gz) used to create your viral filters? If you input the original file used to generate the filters you should get a match so that is...

The results suggest hb7 is present and the others have shared hits due to sequence similarity to hb7. As the required coverage for infection is dependent on DNA extraction methods...

The difference of CPU architecture aside (some cpus don't have hyperthreads or will have more than 2 hyperthreads per core). I'm not sure if the physical core vs hyperthreads distiction...

Depending on the system configuration I guess it does make sense to perhaps add a seperate parameter for Abyss to use.

Ideally, it would be similar to whatever longranger basic provides, but I haven't figured out where the RX tags are stored in the FASTQ file generated. Maybe something like this:...

The PNG does not handle transparency (a circos issue) well. The colours are slightly transparent. Try to open the SVG that is also produced. The program will have to render...

Good idea. I've only added something to conda once before so I'll need to refresh myself on how to do it again.

Hopefully, it should be seamless since Circos is on conda but I actually had some issues with getting Circos installed via conda working that I hope wasn't a common issue.