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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).

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    $\begingroup$ Would QUAST work on your data? It runs MUMmer and reports coverage. $\endgroup$ – user172818 Aug 4 '17 at 15:21
  • $\begingroup$ Good suggestion @user172818. I'll investigate. $\endgroup$ – bedeabc Aug 4 '17 at 19:17
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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.

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  • $\begingroup$ 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. $\endgroup$ – bedeabc Aug 11 '17 at 18:31

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