I developed own DNA assembly pipeline. Input is set of reads and output is set of contigs. Many papers measure own algorithms and compare it against each other. There are basic metrics like:

  • N50, N70..,
  • number of contigs,
  • genom coverage,
  • error rate

I download tool QUAST and there I can see metric N50, L50, where is easy to develop own computation. But how I can measure error rate of my output contigs? Is there any tool which can do it? I searched in many papers but I cannot find way how they do it. I would like to compare with some assemblers with some general way. I found only hints that it should be done by aligning contigs to reference genomes but I do not know how and if it is right way.

  • $\begingroup$ This is just data parsing. You can use simple scripts for this. $\endgroup$ – WYSIWYG Nov 25 '15 at 5:39
  • $\begingroup$ Can you please describe more, or some example? $\endgroup$ – rbrisuda Nov 25 '15 at 12:59

If you are interested on the topic of how to compare assemblers, have a look at assemblathon. That group has two papers and working on a third about comparing genome assembly algorithms.

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