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Old 04-19-2011, 02:20 PM   #1
allo
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Default PacBio AHA hybrid assembler

Anybody out there with experience on how to run the PacBio AHA hybrid de novo assembler? I just downloaded the PacBio SMRT-pipeline software and I just cannot find any instructions on how to do it. I read all the READMEs, "index.htlm" and PDFs on the package.
I want to do an Illumina/ PacBio assembly of a bacterial genome.

Thanks!
AlLo
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Old 04-21-2011, 01:30 PM   #2
allo
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OK, I dislike answering my own posts but this info may be important to others. The instructions for the SMRT-pipeline are in a document appropriately entitled “SMRT Pipe Reference Guide” on the Algorithms page at the PacBio DevNet website http://www.pacbiodevnet.com/Algorithms. The instructions on how to write the XML files that the pipeline requires are not for Biologists . If you have experience with XML or writing HTML you can do it. I come from the Bio world and it took me four tries to get the pipeline to run. I used the default parameters from the ‘longreads’ example but I would love to have a better explanation for some of these values . I guess I’ll have to play with them and learn from the results although this could get very time consuming. Cheers!
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Old 02-04-2013, 12:49 PM   #3
sagarutturkar
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Quote:
Originally Posted by allo View Post
OK, I dislike answering my own posts but this info may be important to others. http://www.pacbiodevnet.com/Algorithms.
Indeed, keep answering your own post if you have figure out the solution. It help others. Its easy for me to do a quick search on seqanswers rather than searching bunch of pacbio pages. Thanks.
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Old 02-19-2013, 08:07 AM   #4
sagarutturkar
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Default XML files for AHA

HI,

I have SMRTanalysis pipeline installed but struggling to get it running correctly. I guess some error with XML files creation.

Can you please provide any pointers regarding this or post xml files that worked for you.

Thanks
Sagar
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Old 02-19-2013, 08:17 AM   #5
GenoMax
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Sagar,

Do you have the web interface for SMRTanalysis installed? If you do then try running the test data set analysis through that interface and check if it completes successfully. If it does (it should, if you have things correctly installed) then grab the XML file from that run as a working example.

We had spent some time on trying to get the command line PacBio tools to work (albeit a year or so ago) but could never get them to work right. We finally gave up on that effort and switched to using the web interface.

Perhaps the disconnect between the web based SMRTanalysis and the command line tools is still there in the latest version. If I have time I will try to check on that.
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Old 02-20-2013, 11:33 AM   #6
flxlex
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Have a look at the xml files in the installation here /opt/smrtanalysis/common/protocols/ (or $SEYMOUR_HOME/common/protocols/), especially RS_AHA_Scaffolding.1.xml. See also my answer at this thread: http://seqanswers.com/forums/showpos...27&postcount=2
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Old 10-22-2013, 09:54 PM   #7
zhoufan
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Hi everyone,
I am trying AHA for scaffolding the contigs assmbled from illumina reads,the P_filter moudule runs well,but when run HybridAssembly module , an error "invalid literal for int() with base 10: ' ' ",it seems like it's a problem relates with python. By the way,i am using smrtPipe v2.0.1 on ubuntu 10.04.
can any body help?thanks.
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Old 10-23-2013, 05:41 AM   #8
sagarutturkar
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Hi zhoufan,

It seems like formatting issues with your contig assembly. Are you transferring these files between windows and linux? That might be the issue. Another way is to format your assembly with FASTX toolkit - FASTA Formatter (http://hannonlab.cshl.edu/fastx_tool...mmandline.html).

Also, make sure your fasta headers are kept at minimum length and does not have special characters.

I am not sure if this will work, but worth trying.

Thanks
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Old 10-23-2013, 05:48 AM   #9
sagarutturkar
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Also you should look at the thread
http://seqanswers.com/forums/showthr...7090#post97090 and reply #21 onwards.
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Old 10-28-2013, 02:03 AM   #10
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Hi sagarutturkar,
Thanks for your help! The problem is there have space in the fatsta header.
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