Contig Assembly Software?

Ashok Aiyar aiyar at ebv.oncology.wisc.edu
Mon Oct 5 17:45:37 EST 1998


On Mon, 05 Oct 1998 17:10:33 -0700,
    R. John Lye (rjl6n at Virginia.edu) wrote:

>     I was wondering if there are any good programs for the
>PC that will do contig assembly from sequence data?  I use
>GeneRunner for most of my mol. biol. work, but version 3.04,
>which seems to be the most recent version, does not have the
>sequence assembly module implemented.  Thanks.

There are several; let me point you toward two that I am familiar with:

a) DNAstar (from Lasergene http://www.dnastar.com).  I have used
   DNAstar on Macs, and it works quite well.  The Mac and Windows 
   versions share a common GUI, and run about $1500.00.

b) If you prefer a command line interface, then the best possible
   solution is to obtain PHRED and PHRAP from Brett Ewing and David
   Gordon from the Univ. of Washington.  Both programs are free for
   academic users.  PHRED and can read ABI and SCF format files, do the 
   base-calling and save the base-called output.  PHRAP can assemble a 
   contig from the PHRED output, and assign a quality for each position 
   in the contig.  Together they can work in batch.
   PHRAP and PHRED are only available as source code, but they compile
   and work well under many platforms, including Windows NT 4.0 and
   Windows 95.  I have compiled Win32 binaries of each using the free
   cygwin32 compiler (http://www.cygnus.com/gnu-win32).

Ashok
-- 
Ashok Aiyar, Ph.D.
McArdle Laboratory for Cancer Research
aiyar at ebv.oncology.wisc.edu



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