Consed--A Finishing Package (Editor, Autofinish, Autoreport, Autoedit, and Align Reads To Reference Sequence)

Return to the Phred/Phrap/Consed System Home Page

Contents

• Why Use Consed?
• Published References
• Consed Current Features
• Supported Platforms
• How to Get Phred/Phrap/Consed
• Documentation

Why Use Consed?

• Supports Solexa, 454, and Sanger Reads and allows mixtures of these read types
• Consed has been used with assemblies of 10s of millions reads--there is no built-in limit.
• Consed is compatible with Newbler, Cross_match, Phrap and PCAP output.
• Quickly takes the user to each variant site for viewing (also available as an automated report)
• Consed is licensed to over 4000 sites and climbing. In *active* use at over 230 sites in 36 countries including biotech, chemical, pharmaceutical, and agricultural companies, major genome centers, small academic labs, and government labs
• Editing time reduced by the program's ability to pin-point problem areas
• Editing is guided by error probabilities
• Consed is able to pick primers very successfully (98 out of 98 in a controlled study). Labs that use it are quite happy with it.
• Able to pick PCR primers to amplify a region, even if you only have a fasta file for the region
• Can compare assembled sequence to restriction digest
• Overview of assembly can help detect and fix misassemblies

Published References

Gordon, D., C. Desmarais, and P. Green. 2001. Automated Finishing with Autofinish. Genome Research. 11(4):614-625.

Ewing B, Hillier L, Wendl M, Green P: Basecalling of automated sequencer traces using phred. I. Accuracy assessment. Genome Research 8, 175-185 (1998).

Ewing B, Green P: Basecalling of automated sequencer traces using phred. II. Error probabilities. Genome Research 8, 186-194 (1998).

Click to see Current Consed Features

Click to learn about Autofinish

Supported Platforms

• Linux (32 bit--i686, i386. Type uname -a)
• Linux (64 bit--AMD64 and EM64T, x86_64. Type uname -a)
• Linux Itanium (ia64. Type uname -a)
• Mac Macosx (powerpc. Type uname -a)
• Mac Macosx (i386. Type uname -a)
• Sun Solaris (Sparc) (2.7 or better)
• Sun Solaris (x86, Intel) (2.8 or better)

The following platforms are currently not supported:

• Microsoft Windows of any flavor (e.g., XP, 2000, NT, etc.)

Consed is written in C++ using Motif and X.

How to Get Phred/Phrap/Consed

1. Phred and Phrap are emailed to you. Consed is not emailed to you--to get it you must email David Gordon the information requested in the academic user agreement including the number you get by clicking here. After you get an email reply from David Gordon that he has given you access from that computer, you download consed yourself in step 5 (below).

   (If I have already given your ip address web access, you will still have that access and can proceed to step 5) to download the new version of Consed.)

   If we have not yet given you web access:

2. If you are an academic user of Phred/Phrap/Consed, read the following academic user agreement and follow the instructions in it. We are supposed to be picky about your following those instructions--if you don't, the agreement will be returned to you. So save yourself time by reading the entire agreement the first time.

3. If you are a commercial user of Phred/Phrap/Consed, there is a fee of roughly $10,000 for the entire Phred/Phrap/Consed for as many users, as many computers, and as many kinds of computers as you want at a particular site. (This fee is used to help support further Phred/Phrap/Consed development.) For the correct current price and details, you should contact swxfr (at) u.washington.edu or see UW TechTransfer Digital Ventures' Direct Licensing.

   If you have any technical questions or problems, feel free to contact us (replace the " at " with "@"):

   • dgordon at u.washington.edu for Consed
   • phg at u.washington.edu for Phrap
   • bge at u.washington.edu for Phred

4. When you have returned by email the license (above) with the ip address, platform, and all other information requested, I will allow your browser access. You will then be able to open url:

   http://bozeman.mbt.washington.edu/consed/consed.html

   and click on the appropriate bundle. Save it to a file.

   How to determine whether you have 64 bit linux, 32 bit linux, or itanium linux?

   click here to download the .tar.gz file for most Linux computers (i686, i386, EM64T, AMD64, ia64)
   (size: 29835559)

   click here to download the .tar.gz file for Macosx (powerPC or i386)
   (size: 17629074)

   click here to download the .tar.gz file for Solaris
   (size: 14558492)

   click here to download the .tar.gz file for Solaris-x86/Intel (This is not normal Solaris--that is above.)
   (size: 14762879)

   click here to download the .tar.gz for the Consed source code.
   (size: 6867357)
   (We advise against using the source code. We advise instead to download one of the executables above. Building Consed from source is error prone and not simple which is why I provide executables. Due to time limitations I cannot provide any assistance in building Consed. Even if you do not modify the source, you may introduce errors due to using a different version of the compiler, a different version of Motif, different versions of other libraries than I used, etc. For this reason, if you discover Consed bugs, I can only offer help with those bugs if you first reproduce those bugs with an executable provided by me--not an executable you have built. Modifying Consed is also difficult. Although Consed is modular, some modules are used by many other modules. Thus making a change in one place can have unforeseen effects on many other features. It may takes months for you to notice these other side-effects which may not seem connected at all. It is not feasable for me to provide help with modifying Consed sources because of the potentially huge amount of time involved. Then why do we even provide the sources? Due to popular demand.)

   Files fixed after consed released:

   click here to download files fixed after consed was released
   -------------------------------------------------------------------------
5. Some people have had problems with their browser timing out and closing the file before they have completely received it. This problem is unlikely to occur now. But to be sure, type:

   ls -l

   to see the size of the transferred file. Look on the web page to see how large the file should be. If the file is not completely transferred, then try again. If you try 3 times and still can't get a complete copy, notify me at dgordon at u.washington.edu

   After you download the executable, terminate your browser. A browser will compete with Consed for resources.

6. zcat consed_(whichever).tar.gz | tar -xvf -

   (This MUST be done on a Unix, not Windows, computer due to extra characters that Windows puts on every line.)

7. follow the instructions in README.txt. README.txt is created by the command above and will be found in your current directory.

Documentation

Why You Should Get the Latest Version

How to determine whether you have 64 bit linux, 32 bit linux, or itanium linux?

Type:
uname -a

If it says something like this:

Linux lake.interim.stanford.edu 2.6.9-78.0.1.ELsmp #1 SMP Tue Jul 22 18:11:48 EDT 2008 i686 i686 i386 GNU/Linux

where there is an "i686" or "i386", then you have 32 bit linux.

If it says something like this:

Linux lake.interim.stanford.edu 2.6.9-67.ELsmp #1 SMP Wed Nov 7 13:56:44 EST 2007 x86_64 x86_64 x86_64 GNU/Linux

where there is an "x86_64" present, then you have 64 bit linux.

If it says something like

Linux lake.interim.stanford.edu 2.4.21-sgi240rp04041413_10065 #1 SMP Wed Apr 14 13:09:51 PDT 2004 ia64 unknown

where there is an "ia64" present, then you have itanium linux.

Snp-annotated Genome

Author