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
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 -
-
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 -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, 04-11-2024, 12:08 PM
|
0 responses
24 views
0 likes
|
Last Post
by seqadmin
04-11-2024, 12:08 PM
|
||
Started by seqadmin, 04-10-2024, 10:19 PM
|
0 responses
25 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 10:19 PM
|
||
Started by seqadmin, 04-10-2024, 09:21 AM
|
0 responses
21 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 09:21 AM
|
||
Started by seqadmin, 04-04-2024, 09:00 AM
|
0 responses
52 views
0 likes
|
Last Post
by seqadmin
04-04-2024, 09:00 AM
|
Comment