Question: Low coverage genome simulation
1
gravatar for MMK
6.0 years ago by
MMK20
Sweden
MMK20 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 COMMENTlink modified 2.2 years ago by Gabriel R.2.8k • written 6.0 years ago by MMK20
1
gravatar for coleman_jonathan
6.0 years ago by
European Union
coleman_jonathan440 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 COMMENTlink written 6.0 years ago by coleman_jonathan440
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 COMMENTlink modified 2.2 years ago • written 2.2 years ago by Gabriel R.2.8k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1708 users visited in the last hour
_