Low coverage genome simulation

Question

[MMK]

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

Answer 1

[coleman_jonathan]

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

Answer 2

[Gabriel R.]

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.