replacing bwa with minimap2

CAFS-bioinformatics / LR_Gapcloser

use long sequenced reads to close gaps in assemblies

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replacing bwa with minimap2 #2

Open mictadlo opened 5 years ago

mictadlo commented 5 years ago

Hi, Have you tried to replace bwa with minimap2?

Michal

francicco commented 5 years ago

I actually just did it! The pipeline is in shell script, pretty easy to edit. F

andreaswallberg commented 4 years ago

Hi @francicco !

Did it work well using minimap2 and can you share your script?

francicco commented 4 years ago

Hi @andreaswallberg

This is how I did it:

LR_Gapcloser.sh.gz

Cheers F

gringer commented 4 years ago

Might be worth considering Winnowmap as well, because it adjusts selection weights for minimisers based on their frequency, rather than excluding them entirely. This gives less-biased mapping, especially in areas containing highly-repetitive sequences.

LandiMi2 commented 2 years ago

Hey, @francicco I am trying your code using minimap2 but don't seem to work okay. Apart from the script, did you have other scripts?