Parameters for plant genomes

[kkrizanovic]

Hello,

I know this might not be a real issue, but I didn't know where else I could ask. I was wandering if anyone has any advice in using hifiasm for assembling plant genomes.

I have about 25X coverage with PacBio HiFi reads (and about 100X Hi-C reads). The genome in question is about 4Gbp, its not precisely known, and is diploid. I'm sure what the actual plant name is.

I've run hifiasm with default parameters and got 3.7 Gbp assembly with about 3100 contigs.

Does anyone have any parameters settings that should work well with plants that I could try?

[chhylp123]

Do you expect a larger assembly or some other issues?

[kkrizanovic]

I'm not sure about the assembly size, but I would like to get larger contigs :).

[lh3]

Your HiFi coverage is quite low. This will significantly affect the contiguity.

[HenrivdGeest]

I often get thousands of contigs with plants, even those with n50 in tens of mB's. And in my experience, only the minus L parameter for purging has a significant effect on the n50. The best parameter to tweak is more or longer hifi data...

On Fri, 24 Sep 2021, 16:00 Krešimir Križanović, @.***> wrote:

I'm not sure about the assembly size, but I would like to get larger contigs :).

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