What are the best metrics for assessing assembly quality for a de novo genome assembly in a species with no sequenced closely related organisms?
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
-
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
Latest Articles
Collapse
-
by seqadmin
The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.
Avian Conservation
Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...-
Channel: Articles
03-08-2024, 10:41 AM -
-
by seqadmin
Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...-
Channel: Articles
02-26-2024, 02:07 PM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, 03-14-2024, 06:13 AM
|
0 responses
32 views
0 likes
|
Last Post
by seqadmin
03-14-2024, 06:13 AM
|
||
Started by seqadmin, 03-08-2024, 08:03 AM
|
0 responses
71 views
0 likes
|
Last Post
by seqadmin
03-08-2024, 08:03 AM
|
||
Started by seqadmin, 03-07-2024, 08:13 AM
|
0 responses
79 views
0 likes
|
Last Post
by seqadmin
03-07-2024, 08:13 AM
|
||
Started by seqadmin, 03-06-2024, 09:51 AM
|
0 responses
68 views
0 likes
|
Last Post
by seqadmin
03-06-2024, 09:51 AM
|
Comment