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Question: Low coverage genome simulation
1
gravatar for MMK
6.0 years ago by
MMK • 20
Sweden
MMK • 20 wrote:

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
simulation genome • 1.3k views
ADD COMMENT • link •
modified 2.2 years ago by Gabriel R. • 2.8k • written 6.0 years ago by MMK • 20
1
gravatar for coleman_jonathan
6.0 years ago by
coleman_jonathan • 440
European Union
coleman_jonathan • 440 wrote:

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
ADD COMMENT • link written 6.0 years ago by coleman_jonathan • 440
0
gravatar for Gabriel R.
2.2 years ago by
Gabriel R. • 2.8k
Danmarks Tekniske Universitet
Gabriel R. • 2.8k wrote:

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.
ADD COMMENT • link modified 2.2 years ago • written 2.2 years ago by Gabriel R. • 2.8k
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