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
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, 05-10-2024, 06:35 AM
|
0 responses
20 views
0 likes
|
Last Post
by seqadmin
05-10-2024, 06:35 AM
|
||
Started by seqadmin, 05-09-2024, 02:46 PM
|
0 responses
24 views
0 likes
|
Last Post
by seqadmin
05-09-2024, 02:46 PM
|
||
Started by seqadmin, 05-07-2024, 06:57 AM
|
0 responses
21 views
0 likes
|
Last Post
by seqadmin
05-07-2024, 06:57 AM
|
||
Started by seqadmin, 05-06-2024, 07:17 AM
|
0 responses
21 views
0 likes
|
Last Post
by seqadmin
05-06-2024, 07:17 AM
|
Comment