Consed--A Graphical Tool for Editing Phrap Assemblies

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Contents

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

Why Use Consed?

• Consed/Autofinish have been used fine with assemblies of up to 10 megabases (Consed has no built-in limit, but larger assemblies take longer to load)
• Consed is compatible with both Phrap and PCAP output. Consed was developed in parallel with Phrap to take advantage of all information provided by Phrap.
• 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
• Uses a more efficient method of editing
• 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
• Consed includes Autofinish which will automatically choose finishing reads, speeding up finishing and making it cheaper. (See below for success data on Autofinish and also see Genome Research, April 2001 for a paper on Autofinish.)

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).

Consed Current Features

Autofinish

Autofinish Performance

Why Use Autofinish?

Supported Platforms

• Linux (regular 32 bit) (kernel 2.4 or better. Type uname -a)
• Linux Itanium (64 bit)
• Linux AMD64 and EM64T
• Sun Solaris (Sparc) (2.5.1 or better)
• Sun Solaris (Intel) (2.8 or better)
• Mac Macosx (Darwin Kernel Version 6.4 or better)
• DEC-Alpha Digital Unix (OSF1 V4.0 or better)
• IBM AIX 5.2 or better (Type: uname -vr and it should say "1 5" or later.)

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 which platform(s) you want and your ip address. After you get an email reply from David Gordon that he has given your ip address access, 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@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 "@"):

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

4. When you have email returned the license (above) with your ip address, platform, and all other information requested, I will allow access from your ip address and you can proceed to step 5 (below).

5. After you have received an email message saying that you have access, open url:

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

   and click on the appropriate executable. Save it in a file named consed.tar.Z. Let me know if you have any problems.

   click here to download the .tar.Z file for Linux (regular 32 bit)
   (This version was fixed on February 14, 2008 to fix problems with cut/paste, text fields, and right-mouse click.)
   (size: 15623345)

   click here to download the .tar.Z file for AMD64 and most 64-bit Linux computers (EM64T)
   (size: 19187597)

   click here to download the tar.Z file for Itanium 64 bit Linux (This is not normal linux. That is above.)
   (size: 20426493)

   click here to download the .tar.Z file for Solaris
   (size: 25336012)

   click here to download the .tar.Z file for Macosx
   (This version was fixed on January 3, 2008 so it can work with Macosx 5.x (Leopard))
   (size: 17910295)

   click here to download the .tar.Z file for IBM AIX
   (size: 14998277)

   click here to download the .tar.Z file for DEC-Alpha
   (size: 27303763)

   click here to download the .tar.Z file for Solaris-Intel (This is not normal Solaris--that is above.)
   (size: 18397662)

   click here to download a fixed version of sff2scf.c which is for reading 454 reads
   (size: 4496)

   click here to download the .tar.Z for the Consed source code. (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.)
   (size: 3850295)

   -------------------------------------------------------------------------

6. Some people have had problems with Netscape (or any other 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 gordon@genome.washington.edu

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

7. zcat consed_(whichever).tar.Z | tar -xvf -

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

8. 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

Author