Need some help with PacBioToCA

[vince_foray]

Hello everybody,
I'm a novice in genome assembly (and particularly with illumina and pacbio data) and I'm working on the genome of a symbiotic bacteria.

For the moment, I tried hybrid assemblies with MIRA using Pacbio corrected seed reads (from HGAP2) and Illumina paired-end and mate pair reads. Now, I would like to correct my Pacbio long-reads with my Illumina data but I need some helps to perform this task. I know that there are advices on the SourceForge page but it is unclear for me. Briefly, I don't understand how install and use the PacbioToCA pipeline !

Thanks in advance for your help.
Vincent

[rhall]

Given that you have HGAP2 results, I'm guessing you have SMRT Analysis installed? If so you have all the components installed to run PacBioToCA. It is also available as a protocol in SMRT Portal, which is probably the easiest way to run. PacBioToCA (now PBcR) has been updated since the version included in SMRT Analysis and it is probably worth while using the new (8.1) version. Instructions for install:

http://sourceforge.net/projects/wgs-assembler/files/wgs-assembler/wgs-8.1/

It is available as executables so is straightforward to install. It should then be possible to follow:

http://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=PBcR

You can find some test data:

http://www.cbcb.umd.edu/software/pbcr/original/index.html

[pag]

My notes to get 8.1 to work within the SMRT analysis pipeline are on this forum. Obviously if running on command-line outside of SMRT analysis, you won't need all of these.

Here are the relevant bits:
#installing current version of wgs...
sudo mv $DOWNLOADPATH/wgs-8.1-Linux-amd64.tar.bz2 $SMRT_HOME/install/smrtanalysis-2.1.1.128549/analysis/bin
cd $SMRT_HOME/install/smrtanalysis-2.1.1.128549/analysis/bin
sudo tar xjf wgs-8.1-Linux-amd64.tar.bz2 #creates wgs-8.1 directory and fills it
mv wgs-7.0/ wgs-7.0.0 #or wgs.old
sudo ln -s wgs wgs-7.0 #points files that depend on wgs7.0 in the path to a generic "wgs" which will be the current version. hopefully pacbio will eventually switch all files to point to a generic/current wgs directory
sudo ln -s wgs-8.1/ wgs #points the generic to the most up-to-date
sudo chown -h smrtanalysis:smrtanalysis wgs* #changes links' ownership
sudo chown -R smrtanalysis:smrtanalysis wgs-8.1/
sudo chmod -R ug=rX,o-rwx wgs-8.1/