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What are the best metrics for assessing assembly quality for a de novo genome assembly in a species with no sequenced closely related organisms?
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Hi, I am struggling with the same problem. But I am using QUAST which gives n50 length and other metricsOriginally posted by casim View Post -
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.Comment
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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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