Consed/Autofinish is the finishing portion of the
Phred/Phrap/Consed/Autofinish package.

Consed 13.0 is now available.


Every Consed/Autofinish site should immediately discontinue using
older versions of Consed/Autofinish that contain bugs fixed in Consed
13.0.  Older versions of Consed/Autofinish are no longer supported.


WHAT IS NEW IN CONSED 13.0

There has not been a new release for a long time, so all the new and
powerful features are thus available at once.


MACOSX and IBM AIX are now supported

Assembly View
    Shows sequence matches, just like PrintRepeats, but if you click
    on the arcs, Consed will display the alignment in Compare Contigs,
    ready for you to make a join.

    Read depth is shown (quality 20 read depth).
        
    The user can supply a list of reads to not display.  This would be
    useful, for example, if you knew that a particular plate was
    misnamed and did not want the Assembly View Window cluttered up
    with red lines from the reads from that plate.

    You can use Assembly View to select reads to pull out of their
    contigs and to reassemble.
    
Miniassemblies
    If you believe that phrap has misassembled a region and you want
    to reassemble it with different phrap parameters, you can do that
    within Consed.  When phrap is done reassembling the region, Consed
    will accept the newly reassembled region back into the larger
    assembly.

Compare Contigs Window
    Now there is a quality greyscale.  Why is this important?
    Because when you see a discrepancy, you want to know whether
    it is real (and the regions do not overlap) or just due to low
    quality data (and the regions might overlap).

    You can now align inverted repeats: for example, you can align two
    regions of the same contig in which one of the regions is
    complemented with respect to the other.

    If you make a join, you can now see which reads came from which
    old contig.

    You no longer need to specify how many bases to align--it will
    align as many as are alignable--even if this is a very large
    number.  And it will do this faster than it did before.

Ability to remove a list of reads all at once
    You supply a file of filenames.  Consed will process them all at
    once, either putting each of them into its own contig or removing
    them entirely from the assembly.

AutoEdit: 
    Automated method of chopping off all reads that protrude beyond the
    end of the BAC.  This includes chopping off stolen data, whole genome
    reads, etc.  They are turned to X's.

Restriction Digest
    Now can handle whole genome shotgun reads protruding out from the
    end of the clone end.

    You can complement the vector at the click of a button to see if
    it produces a better match.

Ability to navigate by high quality discrepancies in all contigs.

Many bugs fixed. 




HOW TO GET CONSED:

You are now on step #5.

1)  If we have already given you web access, you will still have that
access and can proceed to step 5) to download the new version.  

If we have not yet given you web access:

2) If you are an academic user, copy the academic agreement from the
web site www.phrap.org, click on Consed and follow the instructions.
(On that web page, see "HOW TO GET PHRED/PHRAP/CONSED/REPEATMASKER"
and see item number 2.)  This agreement says basically that you will
not use Phred/Phrap/Consed for any commercial purpose, including
commercially funded sequencing, that you agree not to transfer Consed
to other sites, and that you agree to give to us feedback.)  This
agreement is the same one as for Phrap, so if you have already sent
this to me, consider this step completed.

3) If you are a commercial user, there is a fee (to help support
further Phred/Phrap/Consed development) and you should contact Sue
Dart or Chuck Williams at swxfr@u.washington.edu You can get
Phred/Phrap/Consed quite rapidly if you sign the commercial license
agreement without making any modifications.

4)  Along with the agreement (above), you must send an email message
to gordon@genome.washington.edu with the following 2 pieces of
information:

    A) which type of operating system you are running (solaris 
    2.5.1, 2.6, 7, 8, 9, alpha 3.7, 4.0, sgi 5.3, 6.2, 6.3, 6.4, 
    6.5, or linux (and which flavor of linux) )

    B) the ip address of the computer from which you want to receive
    the file.  This can be any computer on which you can run netscape.
    This computer need not be the same one on which you will run
    Consed.  If you have a firewall, you must also provide me the ip
    address of the firewall--otherwise my webserver may see the ip
    address of your firewall and deny you access.  If you use proxies,
    it may work better if you turn them off.

I will send you back a message that you have access.  Wait for this
response before proceding to step 5.

5)  Using netscape (or some other browser) on the computer you gave me
    the ip address, open url:

www.phrap.org and click on Consed

and then scroll down and click on the appropriate type of computer.
Netscape will ask you what you want to name the file.  Just use the
default.

(If you are denied access, try turning off proxies in netscape.  You
do this with "edit"/"preferences"/"advanced"/"proxies"/"direct
connection to the internet" or "options"/"network
preferences"/"proxies".  If you still have trouble, *carefully* follow
the instructions on the "Don't have a cow, man. You are not authorized
to get this document" page, including the try-to-get-consed part.
Please do not email David Gordon until after you have done followed
these instructions.)

6)  Some people have had problems with netscape 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 transferred 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

7) Transfer the file to a UNIX computer.  Then type whichever of the
following is appropriate for you.  (This depends on, in netscape, when
you saved the file, what name you gave the file).

zcat consed_solaris.tar.Z | tar -xvf -
zcat consed_alpha.tar.Z   | tar -xvf -
zcat consed_hp.tar.Z      | tar -xvf -
zcat consed_sgi.tar.Z     | tar -xvf -
zcat consed_linux.tar.Z   | tar -xvf -

8) Follow the instructions in README.txt included the section labelled
   "INSTALLING CONSED".

Note to whoever is installing this version: There is more to do to
install this version than just replacing the executable.  Please refer
to README.txt with this distribution for details.


All bug reports and suggestions for improvement are appreciated.

You MUST have the following versions in order to use this version of
Consed:

000925.c or later for phred
0.990319 or later for phrap and crossmatch
0.990622.e or later for phd2fasta (supplied with this version of consed)
any version of addReads2Consed.perl  (supplied with this version 
       of consed)
030326 of phredPhrap  (supplied with this version of consed)
       (Note:  if you have an older version of phredPhrap, some of the
       more recent Consed features, such as miniassemblies, will not
       work.)
011130 or later for transferConsensusTags.perl  (supplied with this 
       version of consed)
any verion of tagRepeats.perl  (supplied with this version of consed)
any version of determineReadTypes.perl (or your own custom
       modified version)

If you have modified tagRepeats.perl or addReadsToConsed.perl, fine.
They will be compatible with this latest version of Consed.


If you are using polyphred, you must have polyphred 3.5 or more
recent.  USING AN OLDER VERSION OF POLYPHRED WILL CAUSE SEVERE
PROBLEMS WITH CONSED WHICH WILL APPEAR AS PROBLEMS WITH FILETYPES.

Everything that comes with this version of Consed should replace any
of your files that have the same name.

For Phred, contact bge@u.washington.edu (Brent Ewing)

For Phrap and Crossmatch, contact phg@u.washington.edu (Phil Green)

In order to run the gauntlet of Phred/phd2fasta/Crossmatch/Phrap,
there is a perl script phredPhrap supplied with Consed (above).  YOU
MUST USE THIS PERL SCRIPT. If you try to run each of these programs
directly, you are on your own and you will probably fail.  


8) You may join PHUI, the Phred-Phrap-Consed-Autofinish email users'
    group.  This email list is for people to post questions/problems
    with Phred-Phrap-Consed-Autofinish for other users to answer.  To
    subscribe to PHUI, email a message to: 
    listproc@u.washington.edu
    with no subject and the body of the message should say: 
    SUBSCRIBE PHUI (your name) 

    (For some reason, just SUBSCRIBE PHUI won't work--you must put
    your name.)