it si too slow by running 'bwa mem -x ont2d misassembly-free draft long-reads'

[caixu0518]

Hi,
thank you for the nice pipeline GALA. The main problem i met these days is that the process 'bwa mem -x ont2d' is too slow. It takes me two days but not finished.

I want to know is there any new way for me to quiclkly finish the process of mapping my ont reads to my clean draft contigs?

Best,
Xu

[jiehua1995]

I also had this problem. I really suggest to replace bwa mem with minimap2 or at least bwa-mem2. bwa is too slow. Another option is enable multiple threads, which is now not an available parameters in GALA.