Metagenome Read Simulators

Question

[dlawre14]

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?

Answer 1

[Brian Bushnell]

BBMap's simulator, randomreads.sh, has a metagenome mode; just add the flag "metagenome". E.g.

cat bug1.fa,bug2.fa,bug3.fa > bugs.fa
randomreads.sh ref=bugs.fa out=reads.fq reads=10m len=150 paired metagenome

It also has another tool, "mutate.sh", to create strains from a reference with slight differences. This can be useful when simulating metagenomes.

[GenoMax]

[As of BBmap v. 36.59] randomreads.sh gains the ability to simulate metagenomes.

coverage=X will automatically set "reads" to a level that will give X average coverage (decimal point is allowed).

metagenome will assign each scaffold a random exponential variable, which decides the probability that a read be generated from that scaffold. So, if you concatenate together 20 bacterial genomes, you can run randomreads and get a metagenomic-like distribution. It could also be used for RNA-seq when using a transcriptome reference.

The coverage is decided on a per-reference-sequence level, so if a bacterial assembly has more than one contig, you may want to glue them together first with fuse.sh before concatenating them with the other references.

[shenwei356]

OMG, BBmap can do anything!

[dlawre14]

I hadn't thought of BBMap... I swear that thing does everything now. Thank you!

[chetana]

@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.

[Brian Bushnell]

You would do something like this:

cat bacteria1.fa bacteria2.fa (and so forth) > all.fa
randomreads.sh ref=all.fa out=reads.fq len=150 paired reads=10000000 metagenome

Then it will generate reads with different coverage for each sequence in the reference.

[chetana]

Thanks for the reply Brian. Is there a way to know the coverage of each bacteria in my metagenome? Thank you.

[Andrew Tritt]

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.