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Published 20 hours ago • verified publisher icon nanoporetech

parameters for minimap2

Open inemp opened this issue 1 year ago • 1 comments

Hello,

I am running medaka_consensus -i toMount/alsoGoodDataDiv16.fastq -d toMount/small.fa -o experimentFolder -m r1041_e82_400bps_sup_g615

The first step in the pipeline I notice is minimap2 -I 16G -x map-ont -d /toMount/small.fa.map-ont.mmi /toMount/small.fa

Did you experiment with other parameters of minimap2? If yes, did it have big impact on the result, or regardless of minimap parameters , the pipeline performs always similarly?

I know this is mainly a minimap question, but it is an important step of the pipeline

inemp avatar Jul 22 '22 09:07 inemp

We have not performed a systematic study of the effect of varying the minimap2 parameters recently. However the consensus model in medaka is trained against alignments using the parameters as stated in the helper script.

cjw85 avatar Aug 10 '22 10:08 cjw85