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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?
The text was updated successfully, but these errors were encountered:
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.
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?
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?
The text was updated successfully, but these errors were encountered: