<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>

CC BY-SA 3.0
2017-08-11T18:31:29.583Z
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.
bedeabc
CC BY-SA 3.0
2017-08-10T12:19:49.280Z
2017-08-10T13:14:13.037Z
2017-08-10T13:14:13.037Z
5heikki
<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>

CC BY-SA 3.0
2017-08-04T15:21:18.457Z
Would QUAST work on your data? It runs MUMmer and reports coverage.
user172818
CC BY-SA 3.0
2017-08-04T19:17:33.183Z
Good suggestion @user172818. I'll investigate.
bedeabc
<assembly><coverage>
How to calculate overall reference coverage with MUMmer?
# 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 @user172818. 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.  

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