Answers.Body: <p>I believe all you need to do is to run <code>dnadiff</code> from MUMmer. That will run a comparison and output a number of useful metrics.</p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-08-11T18:31:29.583Z
Answers.Text: Many thanks Devon. The `QRY` field of the `AlignedBases` record in `dnadiff`'s out.report seems to be what I was after. Although clearly a powerful tool, I was surprised how slow dnadiff was to run.
Answers.UserDisplayName: bedeabc
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-08-10T12:19:49.280Z
Answers.LastActivityDate: 2017-08-10T13:14:13.037Z
Answers.LastEditDate: 2017-08-10T13:14:13.037Z
Answers.UserDisplayName: 5heikki
Body: <p>Is the MUMmer suite capable of calculating reference sequence coverage statistics for all query sequences collectively? It would be possible to achieve by parsing the output of <code>nucmer</code> / <code>show-coords</code> / <code>show-tiling</code> but it seems like there should be a better way. I currently do this using a sensitive read mapper, <code>samtools depth</code> and some scripting.</p>
  
  <p>To clarify, I'd like to know the reference coverage achieved using all of the query sequences (i.e. the whole <em>de novo</em> assembly, in my case).</p>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-08-04T15:21:18.457Z
Comments.Text: Would QUAST work on your data? It runs MUMmer and reports coverage.
Comments.UserDisplayName: user172818
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-08-04T19:17:33.183Z
Comments.Text: Good suggestion @user172818. I'll investigate.
Comments.UserDisplayName: bedeabc
Tags: <assembly><coverage>
Title: How to calculate overall reference coverage with MUMmer?
ThreadText: # How to calculate overall reference coverage with MUMmer?
  
  (Asked by: username_0 on 2017-08-03)
  
  Is the MUMmer suite capable of calculating reference sequence coverage statistics for all query sequences collectively? It would be possible to achieve by parsing the output of `nucmer` / `show-coords` / `show-tiling` but it seems like there should be a better way. I currently do this using a sensitive read mapper, `samtools depth` and some scripting.
  
  To clarify, I'd like to know the reference coverage achieved using all of the query sequences (i.e. the whole *de novo* assembly, in my case).
  
  **Tags:** assembly, coverage
  
  > **Comments:**
  > **username_1**: Would QUAST work on your data? It runs MUMmer and reports coverage.  
  > **username_0**: Good suggestion @username_1. I'll investigate.  
  
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  ## 1 answers
  
  ### Answer by username_2 on 2017-08-10. Score: 4 | Accepted answer
  
  I believe all you need to do is to run `dnadiff` from MUMmer. That will run a comparison and output a number of useful metrics.
  
  > **Comments:**
  > **username_0**: Many thanks Devon. The `QRY` field of the `AlignedBases` record in `dnadiff`'s out.report seems to be what I was after. Although clearly a powerful tool, I was surprised how slow dnadiff was to run.  
  
  ---
  
  