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Low coverage genome simulation

Hello!

Is there any program you can recommend me to simulate a genome? I want to simulate a low coverage genome, similar to that obtained from ancient DNA.

Thank you

Cheers
Manuel

genome simulation

2 answers

You could check out PLINK2's simulation function - note that this doesn't simulate the LD patterns that you would find in real data, however - it is worth reading the original PLINK documentation on this as well

We created a set of programs called gargammel that can simulate the reads once you have the fasta file of the genome:

gargammel on github

here is the paper

For simulating demographies, I have been using msprime.

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