[Bio-Linux] viewing 454 assemblies on Bio-Linux

Bela Tiwari btiwari at ceh.ac.uk
Thu Jun 12 07:36:18 EDT 2008


Dear all, 

Recently I sent a post alerting you to the bio-linux-consed package and told you that it was capable of dealing with 454 sequences. Unfortunately, testing this out, followed by email conversations with David Gordon, indicates that this is not the case. Please do NOT follow the instructions in the Consed version 16 instructions for trying  to load a 454 assembly in Consed. 

In brief, if you want to load Newbler assemblies into Consed, you will need to get your data provider to run Newbler with the -consed option. This will allow you to view the assembly, but will still not provide graphical renditions of the reads (i.e. traces). I am in an email conversation with David Gordon about this and will update our bio-linux-consed package as things proceed. 

The good news is that 454 Newbler assemblies can be readily loaded into Staden's gap4 interface, and graphical traces of the reads can be popped up. 

To do this, you will need to convert your 454 assembly with a script available in the new package:

bio-linux-assembly-conversion-tools

After installing that package, converting the assembly format is a one step process:  Run the roche454ace2gap.sh script. An example command line is:

roche454ace2gap.sh -c 10 -p mydbName -v 0 

This script converts the assembly format, and will open up gap4 with your assembly loaded. Further details about what is done by this script and the options you have are given at:
http://envgen.nox.ac.uk/cgi-bin/mt/mt.cgi#staden 


For assemblies to be loaded into Staden, please use Newbler assemblies generated WITHOUT the -consed option. (We haven't tested what happens if you try to load assemblies generated with this option yet. Maybe it works, maybe it doesn't...)

I am currently working on the web page given above, and other web pages relating to 454 data handling. I will post to this list when they are available.


cheers, 

Bela

*************************
Dr. Bela Tiwari
Lead Bioinformatician
NERC Environmental 
Bioinformatics Centre

CEH Oxford
Mansfield Road
Oxford, OX1 3SR
01865 281975

*************************



-- 
This message (and any attachments) is for the recipient only. NERC
is subject to the Freedom of Information Act 2000 and the contents
of this email and any reply you make may be disclosed by NERC unless
it is exempt from release under the Act. Any material supplied to
NERC may be stored in an electronic records management system.





More information about the Bio-linux-list mailing list