Does anyone know if there is a command to increase the input read size for a Newbler de novo assembly? I'm trying to use some 2-3kb PacBio CCS reads, but of course the max input read size is 1,999bp (at least in v2.6, which is what I'm using). Maybe a newer version has this option? Thanks!!!
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
Originally posted by CastleR View PostDoes anyone know if there is a command to increase the input read size for a Newbler de novo assembly? I'm trying to use some 2-3kb PacBio CCS reads, but of course the max input read size is 1,999bp (at least in v2.6, which is what I'm using). Maybe a newer version has this option? Thanks!!!
You should use SMRTAnalysis 2.3 instead
-
Well, if you have enough coverage, HGAPv3 should do a good job. If you have lower coverage, but higher quality CCS reads, than you might be right, Newbler may be a better option for you. Unfortunately I haven't used newbler in many years and can't guide you any further.
What kind of pre-CCS subread coverage do you have? If you have >30X (60X+ would be ideal) then you should just run HGAPv3 with your pacbio subreads.
Comment
Latest Articles
Collapse
-
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 -
-
by seqadmin
The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.
Avian Conservation
Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...-
Channel: Articles
03-08-2024, 10:41 AM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, Yesterday, 06:37 PM
|
0 responses
8 views
0 likes
|
Last Post
by seqadmin
Yesterday, 06:37 PM
|
||
Started by seqadmin, Yesterday, 06:07 PM
|
0 responses
8 views
0 likes
|
Last Post
by seqadmin
Yesterday, 06:07 PM
|
||
Started by seqadmin, 03-22-2024, 10:03 AM
|
0 responses
49 views
0 likes
|
Last Post
by seqadmin
03-22-2024, 10:03 AM
|
||
Started by seqadmin, 03-21-2024, 07:32 AM
|
0 responses
67 views
0 likes
|
Last Post
by seqadmin
03-21-2024, 07:32 AM
|
Comment