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.
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.