CASIM: Assembly Metrics for Assembly quality

[casim]

What are the best metrics for assessing assembly quality for a de novo genome assembly in a species with no sequenced closely related organisms?

[pari_89]

What are the best metrics for assessing assembly quality for a de novo genome assembly in a species with no sequenced closely related organisms?

Hi, I am struggling with the same problem. But I am using QUAST which gives n50 length and other metrics

[Blahah404]

as mentioned, QUAST is a decent one-stop shop with nice visualisations.

You can also check out the Assemblathon 1 and Assemblathon 2 papers for an attempt at objective assessment of different assembly metrics.

There are many metrics but none that is an objective, overall measure of quality. You should therefore think carefully about what you want to do with your assemblies, and choose metrics that support your goal.

That being said, there is one set of metrics which relies on analysing read mapping for plausibility which I think is close to an overall quality metric. It's being developed independently by various groups. One is Vezzi et al. - they are calling the metric Feature Response Curves. Some people at the Broad Institute are working on a similar thing as a way to automatically improve assemblies.