[Bio-Linux] Bio-Linux package for Consed version 16.0 available

[Bela Tiwari]

Hello all, 

Just an email to let you know that we have packaged Consed version 16 for Bio-Linux. It is available on request. (email helpdesk at nebc.nox.ac.uk) 

You need to have a license from David Gordon before we can supply the package to you. Also, bio-linux-consed requires you to have bio-linux-phred and bio-linux-phrap. Both these packages are also available on request, but again, you will need licenses from the providers before we can give them to you. 

Information on getting licenses for these programs is at:

http://www.phrap.org/consed/consed.html#howToGet 

We have put a page about using Consed on Bio-Linux. That page also provides a quick reference for a few features of Consed. 

http://envgen.nox.ac.uk/envgen/software/archives/000578.html 

This version of Consed comes with tools to handle 454 sequences (sff files).  The utilities to handle sff sequences are called sffinfo and sff2scf.  They are run directly on the command line. In essence, they generate scf and phd files of your 454 sequences, (which you can then add to an assembly).
In addition, there is an option in the Add New Reads box that mentions Solexa sequences. (This isn't yet in their documentation though, so I have no idea whether this function is working/supported, etc.)




cheers, 

Bela

 

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

CEH Oxford
Mansfield Road
Oxford, OX1 3SR
01865 281975

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



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