To put together the input file

[vlnaraujo]

I am working on a de novo genome assembly in fasta (originally gfa1). It is not so clear for me how I set up the input file in this situation. Can you help me with that?

Is there any way to set it up with msmc2 in bioconda?

[stschiff]

Hi @vlnaraujo. Yes, MSMC2 is in bioconda.

I think with de novo assemblies you would still use alignment data, but you align all of your short-read data to the de-novo-assembled genome. You can then proceed as usual and make diploid genotype calls.

[vlnaraujo]

Thanks @stschiff ! Do you have any specific recommendation? I am not sure if I get it because I am working on HiFi reads... maybe align the de-novo-assembled genome with my Hifi reads or you mean the subreads?

[stschiff]

I have zero experience with this and don't even know what "HiFi" reads are, I'm afraid.