Currently Bowtie2 is the default backend and is tried first regardless of the input read type, with Minimap2 as the fallback. As Bowtie2 is poorly suited to long reads and long read performance was evaluated with Minimap2 in the paper, Bowtie2 should probably not be the default for long reads.
How I think it should work:
Paired input --> bowtie2 backend by default
Paired input with --aligner minimap2 --> minimap2 with sr preset
Unpaired input --> Minimap2 with map-ont preset
Unpaired input with --aligner bowtie2 --> bowtie2 unpaired mode
I don't think there is a major need to be able to customise away from the map-ont preset for other long read technologies given that we are simply throwing reads out, but this may need to be revisited in future
Currently Bowtie2 is the default backend and is tried first regardless of the input read type, with Minimap2 as the fallback. As Bowtie2 is poorly suited to long reads and long read performance was evaluated with Minimap2 in the paper, Bowtie2 should probably not be the default for long reads.
How I think it should work:
bowtie2backend by default--aligner minimap2-->minimap2withsrpresetmap-ontpreset--aligner bowtie2-->bowtie2unpaired modeI don't think there is a major need to be able to customise away from the
map-ontpreset for other long read technologies given that we are simply throwing reads out, but this may need to be revisited in future