Is there a way to change minimap2 parameters to save memory?

Maggi-Chen / Inspector

A tool for evaluating long-read de novo assembly results

MIT License

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Is there a way to change minimap2 parameters to save memory? #24

Open jwinternitz opened 7 months ago

jwinternitz commented 7 months ago

Hi Maggi,

thank you for the fantastic program! I was wondering if there was a way to change some of the minimap2 parameters within the Inspector.py code? I have some files with >200,000 reads to align to thousands of contigs and I would like to be able to change the -K parameter to 50M to reduce memory consumption. Currently, all my files <180,000 reads complete but over 180K they fail to have reads mapped to contigs because the job gets killed. Any advice?

Jamie

jwinternitz commented 7 months ago

Sorry, I figured it out. I changed the code in Inspector.py to "minimap2 -a -K 50M -Q -N 1 -I 10G -t "

Thanks again for your program!