SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > Pacific Biosciences



Similar Threads
Thread Thread Starter Forum Replies Last Post
Whitelist subreads instead of ZMWs? Aizon Pacific Biosciences 4 03-30-2015 11:03 PM
How to create CCS from subreads without smrtcell data? bastianwur Pacific Biosciences 10 09-22-2014 01:37 AM
Alternatives to Ampliseq Daviesa91 Ion Torrent 3 07-09-2014 04:15 AM
PacBio CCS vs subreads explained ? curious.genome Pacific Biosciences 3 10-24-2013 10:39 PM
Gbrowse Alternatives Amative Bioinformatics 9 02-12-2013 02:14 PM

Reply
 
Thread Tools
Old 10-11-2015, 12:05 PM   #1
danova
Member
 
Location: France

Join Date: Sep 2010
Posts: 27
Default Subreads alignment alternatives

Hi,
Just wondering if anybody has tried to align subreads and build the CCS using alternative alignements programs, others than Blasr.

Iīm thinking of bwa.
The problem is that if you are working with amplicon 16S data and donīt have a reference how would that work. So far bwa mem requires a reference database.


So anybody used alternative alignement programs to build consensus without a reference database ??
danova is offline   Reply With Quote
Old 10-12-2015, 08:54 AM   #2
rhall
Senior Member
 
Location: San Francisco

Join Date: Aug 2012
Posts: 322
Default

Building consensus for a CCS read does not use Blasr. The consensus generation is based on a detailed model of the PacBio error profile. What would be the aim of using an alternate consensus caller?
rhall is offline   Reply With Quote
Old 10-12-2015, 09:04 AM   #3
danova
Member
 
Location: France

Join Date: Sep 2010
Posts: 27
Default

Iīd like to aligne the subreads by other means and compare it to the obtained CSS from the pacbio and evaluate the error rate.
Donīt know how to actually get the error rate as well as number of mismatches, insert and deletions from the bax.h5 files ??
danova is offline   Reply With Quote
Old 10-12-2015, 09:22 AM   #4
rhall
Senior Member
 
Location: San Francisco

Join Date: Aug 2012
Posts: 322
Default

What are you evaluating the error rate of? Without a reference it's impossible to calculate the error rate of the CCS reads.
rhall is offline   Reply With Quote
Old 10-12-2015, 09:26 AM   #5
danova
Member
 
Location: France

Join Date: Sep 2010
Posts: 27
Default

Right I mixed a coupe of things here. Let me explain better
1 / I have sequenced a community mock and generated the CSS. From the CSS i can define the error rate.
2 / Now, I would like to generate CCS by other means and see how the pacbio performs when compared to other alignement programs. I donīt know how to generate the consensus using other soft.

If i donīt compare the pacbio alignement tool to other external soft I donīt know if the CSS generation can be improved.
danova is offline   Reply With Quote
Old 10-12-2015, 10:06 AM   #6
rhall
Senior Member
 
Location: San Francisco

Join Date: Aug 2012
Posts: 322
Default

I don't know of any other program that would be able to generate a consensus even close to the quality of the PacBio CCS algorithm due to the the use of the error profile and complex quality values. The only workflow that may be worth testing is quiver (PacBio's multimolecule consensus algorithm) for that you would have to extract the subreads from a single molecule and run quiver on the subreads, but the CCS algorithm is based on the same concepts as quiver so it is unlikely that the results would be significantly better, as CCS has been optimized for data from a single molecule.
Note PacBio has a new CCS algorithm currently in beta, that generates better results than the current production CCS https://github.com/PacificBiosciences/pbccs although it is not currently usable without direction from PacBio.
rhall is offline   Reply With Quote
Old 10-12-2015, 10:51 AM   #7
danova
Member
 
Location: France

Join Date: Sep 2010
Posts: 27
Default

Thanks,
It looks to me that iīd better wait for Pacbio to work on that and see how it improves over the time. Thanks for the update,
david
danova is offline   Reply With Quote
Reply

Tags
bwa alignments, pacbio

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 12:43 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO