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Sequence correction provided by ONT Research
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parameters for minimap2 #382

Closed inemp closed 1 year ago

inemp commented 1 year ago

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

cjw85 commented 1 year ago

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.