Entering edit mode
7.8 years ago
dlawre14
▴
30
I've been doing some research into simulators for simulating metagenomes and I cannot find a good consensus on what to use. The two big ones I've seen are MetaSim and BEAR. Does anyone have experience with these or others or have any advice for a good meta-genome simulator?
OMG, BBmap can do anything!
I hadn't thought of BBMap... I swear that thing does everything now. Thank you!
@Brian Bushnell : I haven't used BBMap before. But can you please tell how it works when I'm trying to make a simulated metagenome from 10 whole bacterial geneomes and want different abundances of each genome in the metagenome. Thank you so much.
You would do something like this:
Then it will generate reads with different coverage for each sequence in the reference.
Thanks for the reply Brian. Is there a way to know the coverage of each bacteria in my metagenome? Thank you.
Is there anyway to run this so that it's species/isolate aware? The model would be more representative of real communities if it assigned probabilities to species/isolates.