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

Gordon and Green. 2013. Consed: A Graphical Editor for Next-Generation Sequencing. Bioinformatics. Volume 29 Number 22 pp.2936-2937.

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

If you are interested in assemblies that will use 100,000 reads or more, you might need to have a 64-bit computer. I believe any of the above platforms include 64 bit except for regular 32 bit Linux.

The following platforms are currently not supported:

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 swxfr (at) u.washington.edu or see UW TechTransfer Digital Ventures' Direct Licensing. In either case, please cc dgordon (at) uw.edu

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

  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 David Gordon 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: 34,390,726)

    click here to download the .tar.gz file for Macosx (powerPC or i386)
    (size: 21,635,673)

    click here to download the .tar.gz file for Solaris
    (size: 16,615,425)

    click here to download the .tar.gz for the Consed source code.
    (size: 3,078,907)
    (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.

All bug reports and suggestions for improvement are appreciated.


Documentation

Current Release: 27.0      (February 4, 2014)
click here to see the 27.0 announcement
click here to see the 27.0 complete documentation
click here to see additional information after the 27.0 release was completed
click here to see a movie showing gene and conservation tracks in consed
click here for some consed internals

Descriptions of Past Versions

What is new in each version:
what was new in version 8.0      (May 1999)
what was new in version 9.0      (Oct 1999)
what was new in version 10.0     (Aug 2000)
what was new in version 11.0     (Mar 2001)
what was new in version 12.0     (Apr 2002)
what was new in version 13.0     (Apr 2003)
what was new in version 14.0     (Sep 2004)
what was new in version 15.0     (Sep 2005)
what was new in version 16.0     (Sep 2007)
what was new in version 17.0     (Jul 2008)
what was new in version 18.0     (Jan 2009)
what was new in version 19.0     (Feb 2009)
what was new in version 20.0     (Oct 2010)
what was new in version 22.0     (Mar 2012)
what was new in version 23.0     (May 2012)
what was new in version 24.0     (April 2013)
what was new in version 25.0     (June 2013)
what was new in version 26.0     (August 16, 2013)

Author

David Gordon

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