minimap2 loading index and run time

[bernicegu313]

Hi, Thank you for tool @lh3 ! I have a question： My target sequences is a little big (56 G), When I ran a alignment， 9000 reads running for 15 minutes (16 thread), 15G in memory . how can I improve the alignment speed while ensuring that memory does not consume too much?And the parameters I bulid index with : minimap2 -x map-ont -d target.mmi target.fa -I 4G，alignment with ：-x map-ont -a -t 16 --secondary=no -L --split-prefix -c Looking forward to your answer

[lh3]

If you have a large machine, it is always preferred to load the entire reference into memory with something like -I100g. If you only have 9000 reads, you can also map target to reads.