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ndierckx / NOVOPlasty

NOVOPlasty - The organelle assembler and heteroplasmy caller
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Genome Range for chloro #173

Closed anupullanhi closed 1 year ago

anupullanhi commented 3 years ago

Hello, what is the genome range to be given for chloroplast in NOVOPlasty. I am running this pipeline for the first time. There is a difference in base pairs when changing the genome range. The data I am using is of bellflower. Any help regarding this query is appreciated. Thank you

ndierckx commented 3 years ago

Hi,

Depends on the size of your accepted genome. For chloroplast genomes I used to take 120000-200000

ndierckx commented 3 years ago

It will try to circularize the assembly within this range by looking for overlaps on both ends of the assembly