I have a collection of genomic contigs that I want to scaffold using a closely related species' genomic reference as the backbone. I just want to use the reference to orient and space the contigs, and then fill in gaps with Ns. What would be the best (and simplest) way to accomplish that?
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
ABACUS was designed for ordering contigs relative to a reference, and with IMAGE you can fill the gaps with your reads. Both programs are a part of the PAGIT pipeline. In my experience, ABACUS is quite straightforward to use but IMAGE is very buggy; it will change the name of you input files, create lots of temporary files and fail without clear warnings. Also, I recall having to change some of the code with IMAGE to get it working correctly.
-
-
Scaffold_builder (http://www.scfbm.org/content/8/1/23) looks straight-forward and could be a good tool for that purpose. Haven't had the time to test it myself yet though.MSc Bioinformatics student at the Free University Berlin , Germany
Comment
Latest Articles
Collapse
-
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 -
-
by seqadmin
Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...-
Channel: Articles
04-04-2024, 04:25 PM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, 04-11-2024, 12:08 PM
|
0 responses
59 views
0 likes
|
Last Post
by seqadmin
04-11-2024, 12:08 PM
|
||
Started by seqadmin, 04-10-2024, 10:19 PM
|
0 responses
57 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 10:19 PM
|
||
Started by seqadmin, 04-10-2024, 09:21 AM
|
0 responses
53 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 09:21 AM
|
||
Started by seqadmin, 04-04-2024, 09:00 AM
|
0 responses
56 views
0 likes
|
Last Post
by seqadmin
04-04-2024, 09:00 AM
|
Comment