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.
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GouthamAtla
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?
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.
Hi, unfortunately ART does not simulate SNPs. Its just a sequence data simulator.
@Dan D I am not able to simulate 300 bp illumina paired end reads using ART
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