From btiwari at ceh.ac.uk Thu Jun 5 10:30:18 2008 From: btiwari at ceh.ac.uk (Bela Tiwari) Date: Thu, 05 Jun 2008 15:30:18 +0100 Subject: [Bio-Linux] Bio-Linux package for Consed version 16.0 available Message-ID: 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 ************************* -- 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. From btiwari at ceh.ac.uk Thu Jun 12 07:36:18 2008 From: btiwari at ceh.ac.uk (Bela Tiwari) Date: Thu, 12 Jun 2008 12:36:18 +0100 Subject: [Bio-Linux] viewing 454 assemblies on Bio-Linux Message-ID: 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. From ajt at rri.sari.ac.uk Sun Jun 15 07:51:53 2008 From: ajt at rri.sari.ac.uk (Tony Travis) Date: Sun, 15 Jun 2008 12:51:53 +0100 Subject: [Bio-Linux] viewing 454 assemblies on Bio-Linux In-Reply-To: References: Message-ID: <48550259.9020106@rri.sari.ac.uk> Bela Tiwari wrote: > [...] > 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 Hello, Bela. I'm interested in this, but I can't read your web link - It's asking me to login... BTW, I've read a GS20 Newbler assembly into consed OK, using the -nophd option (obviously, no quality values are loaded). FYI, I'm evaluating a development version of the MIRA assembler for Sanger + 454 hybrid assemblies: http://chevreux.org/projects_mira.html This also produces 'ace' files, that can be read using consed (without loading phd files). Tony. -- Dr. A.J.Travis, | mailto:ajt at rri.sari.ac.uk Rowett Research Institute, | http://www.rri.sari.ac.uk/~ajt Greenburn Road, Bucksburn, | phone:+44 (0)1224 712751 Aberdeen AB21 9SB, Scotland, UK. | fax:+44 (0)1224 716687 From btiwari at ceh.ac.uk Mon Jun 16 04:41:54 2008 From: btiwari at ceh.ac.uk (Bela Tiwari) Date: Mon, 16 Jun 2008 09:41:54 +0100 Subject: [Bio-Linux] corrected web link for assembly conversion information Message-ID: Hello all, Last week I sent out an email about loading 454 assemblies into assembly viewing software. The web link I provided for further information was incorrect. It should have been: http://nebc.nox.ac.uk/envgen/software/archives/000581.html For instructions on how to convert 454 assemblies for viewing in gap4, see: http://nebc.nox.ac.uk/envgen/software/archives/000581.html#staden 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. From btiwari at ceh.ac.uk Fri Jun 20 05:03:31 2008 From: btiwari at ceh.ac.uk (Bela Tiwari) Date: Fri, 20 Jun 2008 10:03:31 +0100 Subject: [Bio-Linux] New ARB package on Bio-Linux (07-12-07) Message-ID: Dear ARB users, This is just a note to let you know that the bio-linux-arb package has been updated and now contains the December 2007 release of ARB. Your current names.dat and tcp.dat files should be copied over to the new version automatically. Copies of the old files are held at: /usr/local/bioinf/arb/arb_030822/lib/arb_tcp.dat /usr/local/bioinf/arb/arb_030822/lib/nas/names.dat The new ARB version is available in the package repository now, and should be picked up by your machine tonight. Please let us know if you experience any problems with this package. 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. From btiwari at ceh.ac.uk Thu Jun 26 12:17:30 2008 From: btiwari at ceh.ac.uk (Bela Tiwari) Date: Thu, 26 Jun 2008 17:17:30 +0100 Subject: [Bio-Linux] getting the new ARB package on Bio-Linux (07-12-07) Message-ID: Dear all, Due to a added dependency within the new ARB package, most Bio-Linux machines will not have picked up the latest ARB update (in contrast to my recent email, copied below). To get the new ARB update, please run the following commands and answer the prompts: sudo apt-get update sudo apt-get dist-upgrade cheers, Bela ************************* Dr. Bela Tiwari Lead Bioinformatician NERC Environmental Bioinformatics Centre CEH Oxford Mansfield Road Oxford, OX1 3SR 01865 281975 ************************* >>> Bela Tiwari 06/20/08 10:03 am >>> Dear ARB users, This is just a note to let you know that the bio-linux-arb package has been updated and now contains the December 2007 release of ARB. Your current names.dat and tcp.dat files should be copied over to the new version automatically. Copies of the old files are held at: /usr/local/bioinf/arb/arb_030822/lib/arb_tcp.dat /usr/local/bioinf/arb/arb_030822/lib/nas/names.dat The new ARB version is available in the package repository now, and should be picked up by your machine tonight. Please let us know if you experience any problems with this package. 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.