Metapresence for nanopore metagenomic data?

[brambloemen]

Hi,

Thank you for developing this tool!

Are you considering adapting/updating it for nanopore data as well?
I assume that the main technical issue there would be that the reads often vary (a lot) in length. But as far as I've understood from the paper, I don't think this would change anything fundamentally about the BER and FUG metrics, right?

Cheers,

Bram

[davidesangui]

Hi,

Interesting point; I never actually reasoned about how would the metrics behave with long reads.
Like you said, theoretically it should be the same.
Perhaps a lower number of reads in nanopore libraries may be a problem since, even if the size of the library (in terms of base number) is the same of a given short-read sequencing, the lower number of indipendent points may prevent fron getting accurate metric calculations.

As soon as I have a bit of time I will try to run some simple test and I will get back here.

Thank you for bringing this up.

Davide