Simulation of single-end reads from reference genome

Question

[newscient]

Hi, I am trying to simulate single-end sequencing reads from a reference genome but uniformly distributed. I have the desired read length and number of reads, I could easily use DWMSIM (https://github.com/nh13/DWGSIM) to generate reads randomly, but i am looking for a tool that would make things easier regarding the wanted uniform coverage of the genome?

Thanks in advance!

[Gabriel R.]

what do you mean by "uniform" coverage?

[newscient]

Sampling reads using a uniform distribution sounds better !?

[Gabriel R.]

ok just checking to make sure :-) Because using a uniform dist. the coverage at any given site will be Poisson distributed.

I coded gargammel which is a simulator for ancient DNA:

https://grenaud.github.io/gargammel/

it can be used for modern DNA as well though, just remove the ancient DNA idiosyncrasies. It uses ART to simulate seq errors. I know that ART can simulate different coverage. I do not know if ART can add adapters if the fragment length is less than the read length. gargammel does this though. gargammel also allows you to specify desired coverage.

[d-cameron]

Do you want the probably distribution of read sampling at each position to be a uniform distribution, or do you want uniform coverage across your genome? If you want uniform coverage, then you can't use a random generator. If you want uniform coverage of 50x using 100bp reads then you'll have to generate 1 read every 2 bases; uniform 100x coverage of 100bp reads requires simulating 1 read at each genomic position; and so on.

[GenoMax]

You can also try randomreads.sh from BBMap suite. Check the in-line help for various options.

[d-cameron]

Is the an non-random equivalent? OP appears to want perfectly uniform coverage and to get that you can't use a random sampling strategy.

[GenoMax]

randomreads.sh is the name of the program. It has many options to generate simulated data.

Answer 1

[Sej Modha]

Reads Simulation and Read Simulator