Tweet
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 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
-
While isolating and preparing single cells for sequencing was historically the bottleneck, recent technological advancements have shifted the challenge to data analysis. This highlights the rapidly evolving nature of single-cell sequencing. The inherent complexity of single-cell analysis has intensified with the surge in data volume and the incorporation of diverse and more complex datasets. This article explores the challenges in analysis, examines common pitfalls, offers...Today, 07:15 AM -
Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.
Somatic Genomics
“We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...05-24-2024, 01:16 PM
Comment