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

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Contents

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

Why Use Consed?

• Supports Illumina, 454, other Next-Gen and Sanger Reads and allows mixtures of these read types
• Consed includes BamScape which can view bam files with unlimited numbers of reads. BamScape can bring up consed to edit reads and the reference sequence in targeted regions.
• Consed is compatible with Newbler, Cross_match, Phrap, MIRA, Velvet and PCAP output.
• Quickly takes the user to each variant site for viewing (also available as an automated report)
• Overview of assembly can help detect and fix misassemblies
• 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

Published References

Screen Snapshots for the above Bioinformatics article. (supplementary material, but very important)

Gordon, D., C. Abajian, and P. Green. 1998. Consed: A Graphical Tool for Sequence Finishing. Genome Research. 8:195-202

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)
• Mac Macosx (powerpc. Type uname -a), but bamScape and bam2Ace will not work
• Mac Macosx (i386. Type uname -a). Only version 10.6 and better is fully supported. Older versions must use the powerpc version that doesn't include bamScape and bam2Ace.
• Sun Solaris (Sparc) (version 10). bamScape and bam2Ace will not work.

The following platforms are currently not supported:

• Microsoft Windows of any flavor (e.g., XP, 2000, NT, Vista, Windows 7, etc.)

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

How to Get Phred/Phrap/Consed

1. If you work for a government or educational institution, read the following academic user agreement and follow the instructions in it. We are supposed to be picky about you 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. Email the entire agreement and the information requested including the number you get by clicking here. Email all this to each of the 3 email addresses listed in the agreement.

2. 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 license@uw.edu or see UW CoMotion Express Licensing site. In either case, please cc bge (at) uw.edu

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

   • phg at uw.edu for Phrap
   • bge at uw.edu for Phred and Consed

3. Phred and Phrap will be emailed back to you in separate email messages. Consed will not be emailed back to you. Rather you will get an email message back from Brent Ewing that I have allowed your browser access. You will then be able to click on the appropriate bundle (below) and save it to a file. Note: please don't resend the academic agreement unless more than 2 weeks has passed.

   click here to download the .tar.gz file for most Linux computers (i686, i386, EM64T, AMD64 )
   (size: 36,172,715)

   click here to download the .tar.gz file for Macosx (powerPC or i386)
   (size: 22,148,238)

   click here to download the .tar.gz file for Solaris
   (size: 16,932,854)

   click here to download the .tar.gz for the Consed source code.
   (size: 3,258,845)
   (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.)

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4. 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, try again.

5. create a subdirectory where you downloaded the consed bundle, move there, and unpack the consed bundle:
   1. mkdir consed
   2. cd consed
   3. gunzip -c ../consed_(whichever).tar.gz | tar -xvf -
      where (whichever) depends on the name of the file you downloaded.

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

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

Documentation

Descriptions of Past Versions

Author