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.