I would like to test one of my software for the analysis of Illumina next generation sequencing data. For this reason I would like to create simulated illumina reads starting from a reference genome. Do you know whether a software is available that can perform this task? I would like to work with something that can allow me to create "fake" insertions, deletions, copy number variations and so on. Thank you very much for your help!
DWGSIM is a popular tool and is available from sourceforge at http://sourceforge.net/apps/mediawiki/dnaa/index.php?title=Whole_Genome_Simulation
Thanks Michael! I had a look at the tool and it looks great. I would like to test a new tool particularly with copy number variation and it look like DWGSIM generates only SNP and INDEL. Do you (or anyone else) know a similar tool that can also generate CNV? Thanks!
Don't know any details, but Galaxy has a tool for simulating illumina data.
It's description:
"What it does
This tool simulates an Illumina run and provides plots of false positives and false negatives. It allows for a range of simulation parameters to be set. Note that this simulation sets only one (randomly chosen) position in the genome as polymorphic, according to the value specified. Superimposed on this are "sequencing errors", which are uniformly (and randomly) distributed. Polymorphisms are assigned using the detection threshold, so if the detection threshold is set to the same as the minor allele frequency, the expected false negative rate is 50%."
There are some other tools (that I'm not as familiar with) that you might check:
Pirs: http://www.ncbi.nlm.nih.gov/pubmed/22508794
SimSeq: https://github.com/jstjohn/SimSeq?locale=en
I also would check this old thread on SeqAnswers, where the topic of simulators is discussed: http://seqanswers.com/forums/showthread.php?t=12449
good luck!
I have used "ART simulator" which is hosted by NIH. It has a module to simulate illumina reads. Although, I am not sure if it has a default option on CNV in the simulated reads. But I do know that you can specify your own profiles which will be used in simulation of the reads. It might have what you are looking for. Good luck.
http://www.niehs.nih.gov/research/resources/software/biostatistics/art/
Thanks for that guys! I think a simulator for CNV does not exist though. I just saw the following paper in which the author compare the performance of several CNV finders:
http://www.plosone.org/article/fetchObject.action?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0059128&representation=PDF
They wrote a script to generate a test genome, therefore I immagine such a tool is not available (at least at the time of this paper!)
thanks again!
I really recommend the Flux-simulator ( http://sammeth.net/confluence/display/SIM/Home ). It works perfectly for me.
Hi all,
I have written a utility to simulate structural variations in a genome, and which can be used to simulate CNVs. It takes an annotation of the regions you would like to move, and moves them to a random position in the genome, generating a modified reference. You can choose to simulate copy-paste, cut-and-paste, or excision of the specified annotations, in your case you would want copy-paste.
Then you can generate reads from this modified reference with any of the read simulation tools mentionned previously.
I wrote this tool with the idea of simulating transposon movement, and I can think of a couple of ways you could use it to simulate CNVs of varying copy numbers.
The script can be found at:
http://sourceforge.net/projects/kitchen-drawer/files/sim_SV.py/download
with the usage described here:
https://sourceforge.net/p/kitchen-drawer/wiki/sim_SV.py/
Please contact me if you would like more information!
Best,
Elizabeth
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