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lh3 / minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences
https://lh3.github.io/minimap2
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minimap2 loading index and run time #704

Open bernicegu313 opened 3 years ago

bernicegu313 commented 3 years ago

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 commented 3 years ago

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.