simulation of DNA-Seq paired-end data

Question

[GouthamAtla]

I would like to simulate the dna-seq paired end data with common sequencing errors and snps (diploid organism).

But I do not want to do it on entire fasta file. I have already generated the fragments (300-500bp) using certain protocol. Now I want to generate paired end data from a set of fragments i.e read the fragment from both the ends and include error profile and SNPs so that I can validate the SNP caller I'm interested in.

I would like to know if there is any easier way to do it. Otherwise I need to spend lot of time in writing it from scratch.

Answer 1

[Dan D]

ART should be able to do what you need. When you said this:

But I do not want to do it on entire fasta file. I have already generated the fragments (300-500bp) using certain protocol.

Perhaps I'm misunderstanding, but can't you just make a separate fasta file from these fragments, with each fragment as its own contig? ART can do amplicon-sequencing simulation as well, so maybe that's a feature you could take advantage of?

[GouthamAtla]

Yeah. I have fasta file with fragments as short contains. I thought if I use any simulator, they again try to randomly fragment my contigs and generate fragments. I just want to skip that step.

I will check the amplicon module. Thanks.

[GouthamAtla]

Hi, unfortunately ART does not simulate SNPs. Its just a sequence data simulator.

[dhwani.dholakia]

@Dan D I am not able to simulate 300 bp illumina paired end reads using ART

[GenoMax]

Look into randomreads.sh from BBMap suite. It should be flexible and can simulate SNP, errors etc.

Answer 2

[thackl]

Have a look at simNGS . It comes with two binaries, one creating PE fragments (which you already have) and one that generates reads from fragments (instead of a reference genome).