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Impact of giving genome size instead of estimating it from reads ? #159

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RxLoutre opened this issue Nov 18, 2021 · 0 comments
Open

Impact of giving genome size instead of estimating it from reads ? #159

RxLoutre opened this issue Nov 18, 2021 · 0 comments

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@RxLoutre
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Hello !

I am facing the same issues as mentioned here #133 . As I work with only one species of bacteria, their genome size is always between 6M and 10M. I was toying with the idea to speed up shovill process by giving a sort of "mean" expected genome size to speed up the process and avoid kmc freezes. But what would be the impact if for example I ask for an expected genome size of 7,5 and the genome size is in reality smaller than that ? Would it try to inflate the underlying assembly or not ? How is used this estimated genome size and how far from the actual size the estimation can be ?

Thank you for your help !

Best,

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