Use bwa-mem2 mem to accelerate the pipeline

[tinyfallen]

Hi dear developers,

Thanks for your great work! I noticed the bwa mem had an updated version bwa-mem2 mem which rapidly accelerate the mapping step to half the time before without loss of accuracy. If you get some time, you could test the new version and it may not be a time-consuming task.

Best~

[apredeus]

Just stopped by to post the same thing. Would be pretty helpful for a typical large Hi-C dataset.