assembly software

Mike Parlee mparlee at cts.com
Thu Dec 9 00:48:47 EST 1999

Patriot Nation wrote:

> Thanks for the reply, but 1994 was a long time ago in terms of software.
> The VectorNTI stuff has only been around for a few months (and is likely
> still full of bugs).  DNASTAR has been around for a long time, but has had
> many upgrades and improvements since 1994.  Does anyone have more recent
> experience with these packages?

I used DNASTAR on Macintosh extensively for large (20-40kb +) shotgun
assemblies.  The Macintosh version of SeqMan II (the assembly program) has
been around for a long time and is quite stable.  There were serious
stability issues with other programs in the Lasergene package though.  The
multiple alignment tool (MegAlign) was particularly prone to crash.

My current employer uses Sequencher.  In my experience Sequencher offers some
nice features for small assemblies with low coverage.  Manual edits are
automatically tracked and there are some nice summary views.  When I tried
using Sequencher for large assemblies I was aggravated by the length of time
it took to import each chromatogram.

I am unimpressed with VectorNTI as a sequence assembly tool.  It is excellent
for creating and editing plasmid maps, but the sequence assembly is
definately not there yet.

My favorite sequence assembly tool set would be the Phred/Phrap/Consed trio.
If you are not familiar with the Unix command line the learning curve is
steep, but its availability on Linux means you don't have to invest in
expensive hardware to try it out.  On the plus side, huge alignments go
together in a snap, on the down side you need lots of coverage for reliable
assemblies.  As far as I know there is no way to split contigs or remove
sequences from the assembly.  The selling point for me was assembling a
highly repetitive region of human chromosome (~80kb I think) in just a couple
of hours after a post-doc had been working on it for about a month in

Good luck,

Mike Parlee

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