Answers.Body: <p>Use <a href="https://www.nature.com/articles/s41437-022-00577-3" rel="nofollow noreferrer">existing</a> software to generate simulated fastq files. The input for these tools is generally a set of reference organisms that you'd expect to find in your sample. Simply add your 'engineered' viral genome to the list of references. These tools have error models to simulate all the errors that real sequencing instruments make.</p>
  <p>How you'd go about making a viral sequence recognisable as genetically engineered, I have no clue. I'm sure the person who gave you this assignment has an idea on how to engineer viruses and what recognisable features that would result in, maybe consult with them.</p>
  
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Answers.CreationDate: 2024-03-20T08:19:21.230Z
Answers.LastActivityDate: 2024-03-20T08:19:21.230Z
Answers.UserDisplayName: Pallie
Body: <p>I am an apprentice-level python user who occasionally works in medical laboratories and mainly does business work. I am presented with the unenviable task of orchestrating a proficiency test of some sequencing teams who have the almost equally unenviable task of evaluating metagenomic FASTQ files of wastewater (sewage) data where the question is &quot;could this have been engineered ?&quot;</p>
  <p>Trick: how do you make some FASTQ files that look like wastewater (plenty of those online), definitely has some pathogen (SARS-CoV-2, Ebola, whatever), oh, and the pathogen has to look like it could have been engineered? And make an equal number that do not have the pathogen but otherwise look the same?</p>
  <p>Here is my initial thoughts:</p>
  <ol>
  <li><p>World's simplest version: cat a virus FASTQ onto the end of a
  wastewater FASTQ.</p>
  </li>
  <li><p>change all the identifiers in the virus file so
  they look like a continuation of the wastewater, chop the virus file
  with visual mode in Vim so the reads are the same length as the
  wastewater.</p>
  </li>
  <li><p>instead of cat, do some python to build a new
  FASTQ by randomly selecting lines from the virus and wastewater
  &quot;feedstock&quot; FASTQs.</p>
  </li>
  <li><p>Very fancy: grab a assembled virus FASTA, splice in an interesting
  bit of pangolin, raccoon, pig, etc, then randomly select and subtly
  mutate substrings as reads of appropriate length, and assemble a de
  novo synthetic virus FASTQ. Mix that into the wastewater FASTQ as
  above.</p>
  </li>
  </ol>
  <p>Surely I am missing many, many steps and &quot;very fancy&quot; is probably not that fancy (or maybe the sun will grow cold before it succeeds, I do not know). Help and suggestions welcome, it could be fun.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-03-19T23:00:27.430Z
Comments.Text: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.
Comments.UserDisplayName: Community
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-03-20T22:01:11.270Z
Comments.Text: the pathogen has to look like it could have been engineered  ---> after CRISP editing it could be very difficult to prove that
Comments.UserDisplayName: pippo1980
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-03-21T01:49:46.800Z
Comments.Text: The question needs breaking up into separate questions. I would suggest 3 questions. No-one is going to spend time considering an entire project design in a single question. The whole issue about "is engineered" needs explaining. In reality the project looks relatively easy - but again you are posting an entire project as a single question.
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-03-21T07:10:31.443Z
Comments.Text: The law considers genetically engineered different from genome edited ... please take that onyo your question
Comments.UserDisplayName: pippo1980
Tags: <python><fastq><metagenome><quality-control>
Title: How to design a synthetic wastewater FASTQ file that could be flagged as "engineered"?
ThreadText: # How to design a synthetic wastewater FASTQ file that could be flagged as "engineered"?
  
  (Asked by: username_0 on 2024-03-19)
  
  I am an apprentice-level python user who occasionally works in medical laboratories and mainly does business work. I am presented with the unenviable task of orchestrating a proficiency test of some sequencing teams who have the almost equally unenviable task of evaluating metagenomic FASTQ files of wastewater (sewage) data where the question is "could this have been engineered ?"
  
  Trick: how do you make some FASTQ files that look like wastewater (plenty of those online), definitely has some pathogen (SARS-CoV-2, Ebola, whatever), oh, and the pathogen has to look like it could have been engineered? And make an equal number that do not have the pathogen but otherwise look the same?
  
  Here is my initial thoughts:
  
  1. World's simplest version: cat a virus FASTQ onto the end of a
     wastewater FASTQ.
  2. change all the identifiers in the virus file so
     they look like a continuation of the wastewater, chop the virus file
     with visual mode in Vim so the reads are the same length as the
     wastewater.
  3. instead of cat, do some python to build a new
     FASTQ by randomly selecting lines from the virus and wastewater
     "feedstock" FASTQs.
  4. Very fancy: grab a assembled virus FASTA, splice in an interesting
     bit of pangolin, raccoon, pig, etc, then randomly select and subtly
     mutate substrings as reads of appropriate length, and assemble a de
     novo synthetic virus FASTQ. Mix that into the wastewater FASTQ as
     above.
  
  Surely I am missing many, many steps and "very fancy" is probably not that fancy (or maybe the sun will grow cold before it succeeds, I do not know). Help and suggestions welcome, it could be fun.
  
  **Tags:** python, fastq, metagenome, quality-control
  
  > **Comments:**
  > **username_1**: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.  
  > **username_2**: the pathogen has to look like it could have been engineered  ---> after CRISP editing it could be very difficult to prove that  
  > **username_3**: The question needs breaking up into separate questions. I would suggest 3 questions. No-one is going to spend time considering an entire project design in a single question. The whole issue about "is engineered" needs explaining. In reality the project looks relatively easy - but again you are posting an entire project as a single question.  
  > **username_2**: The law considers genetically engineered different from genome edited ... please take that onyo your question  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_4 on 2024-03-20. Score: 1
  
  Use [existing](https://www.nature.com/articles/s41437-022-00577-3) software to generate simulated fastq files. The input for these tools is generally a set of reference organisms that you'd expect to find in your sample. Simply add your 'engineered' viral genome to the list of references. These tools have error models to simulate all the errors that real sequencing instruments make.
  
  How you'd go about making a viral sequence recognisable as genetically engineered, I have no clue. I'm sure the person who gave you this assignment has an idea on how to engineer viruses and what recognisable features that would result in, maybe consult with them.
  
  
  ---
  
  