The short answer is yes, it does consider both strands.
My recommendation would generally be not to use VCAKE unless you are doing hybrid assemblies of 454 and Illumina data. VCAKE has not been maintained to deal with updates in the technologies, unlike some other algorithms. I would refer to this thread and try algorithms like Velvet, which make use of a more sophisticated graph decomposition method.
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
hi,
i have some vcake questions.
does vcake consider both strands of the input sequence?
i have short reads(31 long) , in my test case they all blat perfectly
to a known genome and there seems to be decent overlap.
but the vcake is not tying the contigs together, i am getting a
max contig of 100 for a 1000 base region
do you have any suggstions?
thanks
jpd
Leave a comment:
-
Hi from Chapel Hill, NC
Hi everyone,
I'm new to the forum today and I love what I see. I've been in next gen sequencing for about two years. I worked on VCAKE, and it's still alive and kicking, now optimized for 454/Illumina bacterial genome assembly ... pipeline forthcoming at vcake.sourceforge.net hopefully in the next few weeks. I can't claim it as my work, but I might as well pump it up a little.
Now I'm an MD/PhD student looking to apply the new genomics to clinical questions (particularly oncology). I've just spent 2 years in medical school so I am all but completely out of the loop, but I'm looking forward to getting back up to speed.
--Will Jeck
UNC Chapel Hill
School of MedicineTags: None
Latest Articles
Collapse
-
by seqadmin
Metagenomics has improved the way researchers study microorganisms across diverse environments. Historically, studying microorganisms relied on culturing them in the lab, a method that limits the investigation of many species since most are unculturable1. Metagenomics overcomes these issues by allowing the study of microorganisms regardless of their ability to be cultured or the environments they inhabit. Over time, the field has evolved, especially with the advent...-
Channel: Articles
09-23-2024, 06:35 AM -
-
by seqadmin
During the COVID-19 pandemic, scientists observed that while some individuals experienced severe illness when infected with SARS-CoV-2, others were barely affected. These disparities left researchers and clinicians wondering what causes the wide variations in response to viral infections and what role genetics plays.
Jean-Laurent Casanova, M.D., Ph.D., Professor at Rockefeller University, is a leading expert in this crossover between genetics and infectious...-
Channel: Articles
09-09-2024, 10:59 AM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, 10-02-2024, 04:51 AM
|
0 responses
13 views
0 likes
|
Last Post
by seqadmin
10-02-2024, 04:51 AM
|
||
Started by seqadmin, 10-01-2024, 07:10 AM
|
0 responses
21 views
0 likes
|
Last Post
by seqadmin
10-01-2024, 07:10 AM
|
||
Started by seqadmin, 09-30-2024, 08:33 AM
|
0 responses
25 views
0 likes
|
Last Post
by seqadmin
09-30-2024, 08:33 AM
|
||
Started by seqadmin, 09-26-2024, 12:57 PM
|
0 responses
18 views
0 likes
|
Last Post
by seqadmin
09-26-2024, 12:57 PM
|
Leave a comment: