How to simulate reads for a number of individuals from one population?

Question

[all.lirik]

Hello!

I would like to provide BAM files consisting of aligned simulated genomic data to one specific model to conduct a small experiment relevant to demographic analysis

To do so, I need to simulate some reads for more than one individual. However, it's important not to make it completely random, since those individuals should belong to one population. Could you give examples of simulation tools that can do such trick?

Thank you guys in advance

Answer 1

[Istvan Albert]

A simple, but not so efficient approach would be to generate a genome for each individual, put those genomes into a single FASTA file then generate reads from all the genomes.

You could generate genomes with

https://github.com/yjx1217/simuG

or by applying a VCF file to an existing genome. For large genomes and large populations, the process could be prohibitively inefficient.

Alternatively, you may look for existing software tools like this GenomePop:

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-9-223

[all.lirik]

Thank you! I'll definitely look through those.

Actually, I found exactly what I needed in ATLAS

It does have some limitations (simulates it's own reference, rather than using the real one as input), but it's still useful for me

[Istvan Albert]

sounds good, thanks for following up with an interesting solution