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 sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...-
Channel: Articles
05-06-2024, 07:48 AM -
-
by seqadmin
The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...-
Channel: Articles
04-22-2024, 07:01 AM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, Yesterday, 06:35 AM
|
0 responses
14 views
0 likes
|
Last Post
by seqadmin
Yesterday, 06:35 AM
|
||
Started by seqadmin, 05-09-2024, 02:46 PM
|
0 responses
18 views
0 likes
|
Last Post
by seqadmin
05-09-2024, 02:46 PM
|
||
Started by seqadmin, 05-07-2024, 06:57 AM
|
0 responses
17 views
0 likes
|
Last Post
by seqadmin
05-07-2024, 06:57 AM
|
||
Started by seqadmin, 05-06-2024, 07:17 AM
|
0 responses
19 views
0 likes
|
Last Post
by seqadmin
05-06-2024, 07:17 AM
|
Comment