Answers.Body: <p><strong>Simulators designed specifically for Oxford Nanopore:</strong></p>
  
  <ul>
  <li><a href="https://github.com/bcgsc/NanoSim" rel="nofollow noreferrer">NanoSim</a></li>
  <li><a href="https://github.com/karel-brinda/nanosim-h" rel="nofollow noreferrer">NanoSim-H</a></li>
  <li><a href="https://github.com/ethanagbaker/SiLiCO" rel="nofollow noreferrer">SiLiCO</a></li>
  <li><a href="https://sourceforge.net/p/readsim/wiki/Home/" rel="nofollow noreferrer">ReadSim</a></li>
  <li><a href="https://github.com/lykaust15/DeepSimulator" rel="nofollow noreferrer">DeepSimulator</a></li>
  </ul>
  
  <p><strong>General long read simulators:</strong></p>
  
  <ul>
  <li><a href="https://github.com/gt1/loresim" rel="nofollow noreferrer">Loresim</a></li>
  <li><a href="https://github.com/gt1/loresim2" rel="nofollow noreferrer">Loresim 2</a></li>
  <li><a href="https://sourceforge.net/projects/fastqsim/" rel="nofollow noreferrer">FASTQsim</a></li>
  <li><a href="https://github.com/bioinform/longislnd" rel="nofollow noreferrer">LongISLND</a></li>
  </ul>
  
  <p>For an exhaustive list of existing read simulators, see page 15 of my thesis, <a href="https://doi.org/10.5281/zenodo.1045317" rel="nofollow noreferrer"><em>Novel computational techniques for mapping and
  classifying Next-Generation Sequencing data</em></a>.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2017-05-29T19:09:21.650Z
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Answers.LastEditDate: 2019-11-17T00:06:26.630Z
Answers.UserDisplayName: Karel Břinda
Answers.Body: <p>By chance, just today I've heard of a nanopore read simulator, <a href="http://biorxiv.org/content/early/2016/03/18/044545.1" rel="noreferrer">NanoSim</a>. It is  <a href="https://github.com/bcgsc/NanoSim" rel="noreferrer">released under a GPL license</a>. I have never used it, though...</p>
  
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Answers.CreationDate: 2017-05-22T20:43:59.303Z
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Answers.UserDisplayName: Leo Martins
Answers.Body: <p>The best nanopore read simulators would be associated with the best base-callers. For a base-caller to effectively model the DNA strand, it needs to take into account the expected underlying electrical model together with the associated signal noise (both in the time dimension as well as the amplitude dimension). In theory, it should be possible to reverse the algorithm and generate an electrical signal given an underlying sequence.</p>
  
  <p>Unfortunately, I'm not aware of any tools that attempt to simulate nanopore reads at the electrical level. Any "nanopore read simulator" that concentrates only on base sequence would need to encompass all the possible base-calling software models that exist, which is an impossible task (particularly given how quickly ONT updates their own base callers).</p>
  
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Answers.CreationDate: 2017-05-24T03:36:03.760Z
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Answers.UserDisplayName: gringer
Answers.Body: <p>In addition to the already mentioned <a href="https://github.com/bcgsc/NanoSim" rel="noreferrer">NanoSim</a>, there is also <a href="https://github.com/ethanagbaker/SiLiCO" rel="noreferrer">SiLiCO</a> and <a href="https://sourceforge.net/p/readsim/wiki/Home/" rel="noreferrer">ReadSim</a> (although it hasn't been updated in over 2 years, so I am not sure how relevant it is at this point considering how fast the technology is progressing).</p>
  
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Answers.UserDisplayName: burger
Body: <p>Are there any free open source software tools available for simulating Oxford Nanopore reads?</p>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-05-22T23:37:08.887Z
Comments.Text: What are you planning on simulating data for? In my opinion, given the wealth of publicly available real datasets, there is little need for simulation except in very specific use cases.
Comments.UserDisplayName: Scott Gigante
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-05-23T02:32:20.983Z
Comments.Text: It's often useful to simulate a variant or some other type of genomic artifact to evaluate whether a tool or set of tools can correctly identify the artifact. This is much easier to do on simulated data where you know the exact answer, and is extremely valuable even if the simulated data isn't a perfect reflection of real data.
Comments.UserDisplayName: Daniel Standage
Tags: <nanopore><genome-sequencing><software-recommendation>
Title: Tools for simulating Oxford Nanopore reads
ThreadText: # Tools for simulating Oxford Nanopore reads
  
  (Asked by: username_0 on 2017-05-22)
  
  Are there any free open source software tools available for simulating Oxford Nanopore reads?
  
  **Tags:** nanopore, genome-sequencing, software-recommendation
  
  > **Comments:**
  > **username_1**: What are you planning on simulating data for? In my opinion, given the wealth of publicly available real datasets, there is little need for simulation except in very specific use cases.  
  > **username_0**: It's often useful to simulate a variant or some other type of genomic artifact to evaluate whether a tool or set of tools can correctly identify the artifact. This is much easier to do on simulated data where you know the exact answer, and is extremely valuable even if the simulated data isn't a perfect reflection of real data.  
  
  ---
  
  ## 4 answers
  
  ### Answer by username_2 on 2017-05-29. Score: 11 | Accepted answer
  
  **Simulators designed specifically for Oxford Nanopore:**
  
  * [NanoSim](https://github.com/bcgsc/NanoSim)
  * [NanoSim-H](https://github.com/username_2-brinda/nanosim-h)
  * [SiLiCO](https://github.com/ethanagbaker/SiLiCO)
  * [ReadSim](https://sourceforge.net/p/readsim/wiki/Home/)
  * [DeepSimulator](https://github.com/lykaust15/DeepSimulator)
  
  **General long read simulators:**
  
  * [Loresim](https://github.com/gt1/loresim)
  * [Loresim 2](https://github.com/gt1/loresim2)
  * [FASTQsim](https://sourceforge.net/projects/fastqsim/)
  * [LongISLND](https://github.com/bioinform/longislnd)
  
  For an exhaustive list of existing read simulators, see page 15 of my thesis, [*Novel computational techniques for mapping and
  classifying Next-Generation Sequencing data*](https://doi.org/10.5281/zenodo.1045317).
  
  
  ---
  
  ### Answer by username_3 on 2017-05-22. Score: 9
  
  By chance, just today I've heard of a nanopore read simulator, [NanoSim](http://biorxiv.org/content/early/2016/03/18/044545.1). It is [released under a GPL license](https://github.com/bcgsc/NanoSim). I have never used it, though...
  
  
  ---
  
  ### Answer by username_5 on 2017-05-22. Score: 7
  
  In addition to the already mentioned [NanoSim](https://github.com/bcgsc/NanoSim), there is also [SiLiCO](https://github.com/ethanagbaker/SiLiCO) and [ReadSim](https://sourceforge.net/p/readsim/wiki/Home/) (although it hasn't been updated in over 2 years, so I am not sure how relevant it is at this point considering how fast the technology is progressing).
  
  
  ---
  
  ### Answer by username_4 on 2017-05-24. Score: 3
  
  The best nanopore read simulators would be associated with the best base-callers. For a base-caller to effectively model the DNA strand, it needs to take into account the expected underlying electrical model together with the associated signal noise (both in the time dimension as well as the amplitude dimension). In theory, it should be possible to reverse the algorithm and generate an electrical signal given an underlying sequence.
  
  Unfortunately, I'm not aware of any tools that attempt to simulate nanopore reads at the electrical level. Any "nanopore read simulator" that concentrates only on base sequence would need to encompass all the possible base-calling software models that exist, which is an impossible task (particularly given how quickly ONT updates their own base callers).
  
  
  ---
  
  