I used AHA in PacBio's smrtanalysis-2.0.1 to scaffold contigs using long-read PacBio data. I now have the output files "scaffold.gml" and "scaffold.fasta". I now realise I have no idea how to use these files and my contigs to generate one long fasta sequence. Can anyone help me out here?
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
Hi schroedj,
The scaffold.fasta should contain the most contiguous sequence that the data and algorithm is able to generate. If it isn't "one long fasta sequence" then you need to look into why you're getting the results you are getting, or if AHA is making any difference. There should be very basic stats on the number of scaffolds created, which you can compare to the number of contigs you supplied. Is this what you are asking about?
We look at:
How large is the genome you are trying to assemble? (AHA is only supported up to 200Mb)
How "good" are the contigs going into the AHA? (number of contigs, contig lengths, %of genome, etc.)
How much PacBio Data are you supplying? (My personal rule-of thumb is to give AHA at least 5x coverage, but 2x coverage is the minimum to get any results at all. That is because the "redundancy" parameter is set to 2 by default. This is the minimum number of reads needed to link two contigs).
The parameters to tune AHA can be found in the smrtpipe reference guide:
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
32 views
0 likes
|
Last Post
by seqadmin
04-11-2024, 12:08 PM
|
||
Started by seqadmin, 04-10-2024, 10:19 PM
|
0 responses
35 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 10:19 PM
|
||
Started by seqadmin, 04-10-2024, 09:21 AM
|
0 responses
30 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 09:21 AM
|
||
Started by seqadmin, 04-04-2024, 09:00 AM
|
0 responses
53 views
0 likes
|
Last Post
by seqadmin
04-04-2024, 09:00 AM
|
Comment