I have the simplest task for a de novo assembler: to assemble a short bacterial 10kb plasmid without repeats from Illumina 90 bp long reads. The plasmid was sequenced on average 1,000 times over. I used default parameters on velvet and SeqMan NGen and couldn't get it assembled. Could anyone suggest an assembler and parameters that I could use for the task.
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
Originally posted by pmiguel View PostFirst throw away 90% of your reads. 1000x is too high.
--
Phillip
Comment
-
Originally posted by e.dobbs View PostI have a similar project to this one and I'm having trouble assembling my viral sequences which I'm expecting 10,000-100,000x coverage. Why does too much coverage produce a problem for de novo assembly?
Travis
Comment
-
Originally posted by e.dobbs View PostI have a similar project to this one and I'm having trouble assembling my viral sequences which I'm expecting 10,000-100,000x coverage. Why does too much coverage produce a problem for de novo assembly?
--
Phillip
Comment
Latest Articles
Collapse
-
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 -
-
by seqadmin
The first FDA-approved CRISPR-based therapy marked the transition of therapeutic gene editing from a dream to reality1. CRISPR technologies have streamlined gene editing, and CRISPR screens have become an important approach for identifying genes involved in disease processes2. This technique introduces targeted mutations across numerous genes, enabling large-scale identification of gene functions, interactions, and pathways3. Identifying the full range...-
Channel: Articles
08-27-2024, 04:44 AM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, Today, 06:25 AM
|
0 responses
13 views
0 likes
|
Last Post
by seqadmin
Today, 06:25 AM
|
||
Started by seqadmin, Yesterday, 01:02 PM
|
0 responses
12 views
0 likes
|
Last Post
by seqadmin
Yesterday, 01:02 PM
|
||
Started by seqadmin, 09-18-2024, 06:39 AM
|
0 responses
14 views
0 likes
|
Last Post
by seqadmin
09-18-2024, 06:39 AM
|
||
Started by seqadmin, 09-11-2024, 02:44 PM
|
0 responses
14 views
0 likes
|
Last Post
by seqadmin
09-11-2024, 02:44 PM
|
Comment