simulating illumina paired end reads

[Splinter479]

I am currently programming a complete pipeline for ddRADseq simulation.
Last step is to create paired end illumina reads.
My problem is, that the most simulators produce their own fragments (mostly random from a give genome) to produce paired end reads.
I like to hand in my own fragments into the tool of cause. I have no use of random fragments.

[dpryan]

There are a number of read simulators out there. I've used Sherman recently, and it works OK. There's also wgsim among many others. There's an old post on Biostars with a number of read simulators that should work.

[vishnuamaram]

Hey Splinter479,

What is your goal of simulating Illumina paired end reads and the purpose of your experiment. Is it sensible to follow this approach.

Regards,
Vishnu.

[Splinter479]

Hello Ladies and Gents,

I am currently trying to simulate illumina paired end reads. Here is the situation:

I have a fasta file containing many DNA fragments of different sizes.
Now I want to simulate paired end reads for each of this fragments including illumina like read errors.

Do you know a tool / solution for this routine? Actually I am only hold back by the illumina read errors to include. In case of necessity I could programm the rest by myself.

Thanks a lot,

Thomas