What are the best methods/programs for attempting to close gaps between scaffolds after a de novo assembly has resulted in a large number of scaffolds (before resorting to further sequencing)?
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
First, I don't know why you've chosen to prefix all your posts with your username; not a desirable strategy.
Second, you've failed to describe any details about the genomes you are working on, the data you've acquired & how you've tried to assemble. The size & complexity of the genome are critical to understand as well what you have in hand and what scientific goals you really want to address.
-
Okay, apologies for the previous comment.
There are a number of scaffolders out there, though I have used only SSPACE and without digging in much.
One thing that would benefit all of these programs is if there was a rigorous language for defining relationships that scaffolding might be based on. Ideally this would a XML; I know many folks aren't XML fans but the value of being able to validate inputs is powerful.
One distinction amongst scaffolders is their modularity. To give two examples, SSPACE is non-modular and must be run en masse. At the other extreme, SGA can apparently be used as a scaffolder & simply takes BAM files and a few parameters.
Comment
Latest Articles
Collapse
-
by seqadmin
Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...-
Channel: Articles
03-22-2024, 06:39 AM -
-
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 -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, Yesterday, 06:37 PM
|
0 responses
8 views
0 likes
|
Last Post
by seqadmin
Yesterday, 06:37 PM
|
||
Started by seqadmin, Yesterday, 06:07 PM
|
0 responses
8 views
0 likes
|
Last Post
by seqadmin
Yesterday, 06:07 PM
|
||
Started by seqadmin, 03-22-2024, 10:03 AM
|
0 responses
49 views
0 likes
|
Last Post
by seqadmin
03-22-2024, 10:03 AM
|
||
Started by seqadmin, 03-21-2024, 07:32 AM
|
0 responses
67 views
0 likes
|
Last Post
by seqadmin
03-21-2024, 07:32 AM
|
Comment