Handling long reads

[nlapier2]

Several people have mentioned their interest in a long read mode of Metalign. The main challenge may be figuring out how to compute containment indices accurately. Minimap2 can obviously handle long reads, with an adjustment to the parameters. For abundance estimation, we'd have to shift to using number of bases mapped instead of read counts as the unit of abundance.

[nilay-p]

Hi,
I was wondering if there is any development with the tool regarding to handling long reads. I am very much interested in using it in place of Kraken2.
What parameters would you suggest to adjust for analyzing long reads with the currrent version of the tool?

Kind Regrads,
Nilay