Minimap2: which mapper to use, and bwa to minimap2 eqiuvalent functions

[devonorourke]

Good morning,
I was wondering if there are equivalent arguments to pass between bwa and minimap2: I'm trying to align some Hi-C data generated by Phase Genomics, and they recommend aligning with bwa using the -5, -S, and -P flags.
I'm not quite sure if it's even better to use minimap2 over bwa, and can appreciate that certain circumstances may favor one mapper over another. Within the hickit example, it shows using bwa as the aligner, but then mentions that it also works with minimap2.
I'm curious if:
a) there are specific minimap2 parameters to pass to make it perform like the -5SP parameters used in bwa mem;
b) there is any reason, other than speed, to use minimap over bwa in this specific mapping circumstance?

Thank you very much

[lh3]

Minimap2 doesn't implement "-S" in bwa-mem. Option "--no-pairing" corresponds to "-P" of bwa-mem. Minimap2 doesn't have a "-5" behavior, but the feature is usually not critical to Hi-C. Hickit doesn't rely on "-5", either.

Hi-C hits are shorter due to split/"chimeric" reads. Bwa-mem is more sensitive to such hits than minimap2 and is thus the preferred choice.

[devonorourke]

Perfect. Thanks for the clarification.