Summary: Software choice? sequencher, phrap/phred/consed, staden?

Don Gilbert gilbertd at chipmunk.bio.indiana.edu
Thu Aug 29 17:37:48 EST 1996

This is a summary of responses to :
	Do you have opinions to share on the best choice(s) of
	software for small-scale autosequencing?  We have recently acquired
	Sequencher, Phrap/Phred/Consed/etal, and Staden package,
	all of which can handle ABI and SCF trace data, do base calling
	and assembly.  But it will take some time to compare and evaluate
	these, so your experiences would be valuable to us and others
	starting with such software.

My thanks to the many people who wrote me or posted a reply. It is
good to see so many helpful people sharing their experiences thru
network news.

The unanimous favorite software was Sequencher.  However only two 
respondents expressed experience with the Unix programs (Phrap & Staden), 
so this does not offer as clear an answer as I had hoped.  Brue Roe's 
helpful sharing of his experience with these packages sounds like good advice.


From: Bruce Roe 

        It depends on the platform as Sequencher is on the Mac and many
folks really like it.  Both for performance and because it's Mac-based.
Phrap/Phred/Consed/etal, and Staden package are all unix based and to
many users, that's a big pain as they don't have readily available unix
boxes.  Sure you can use Mac-X and connect but that too is a pain.
        For small-scale projects I'd strongly recommend Sequencher as
it has many advantages to the end user and because it's commercial, is
supported very very well.  For large projects, go with the unix programs,
however, Consed doesn't have some of the features that we find useful
in XGAP/gap4 for editing contigs.  Both also have GREAT difficulty in dealing
with repeat sequences (especially in cosmids, bacs, pacs, fosmids with 40-
300kb inserts).  The jury is still out on which handles these repeats better
Phred/Phrap or Staden, as Phred/phrap has a tendency to make "false" joins
while Staden's xgap/gap4 refuses to make any false joins so a person has to
use "find internal joins" and then (sometimes or most of the time depending
on experience) makes some bad joins anyway.
        None of these programs is ideal, especially with large projects.
But for the small ones's (2-10kb), I'd go with "simplest is best" and stick
with Sequencher.  I know it costs the most, BUT you get what you pay for
and have someone to gripe at that HAS to be responsive or else they loose

From: lc stillwell 

Since I have been a Mac user for so long I really prefer to use Sequencher when 
I can but the capacity of the program combined with my power mac is somewhat 
limited. It is very easy to learn and use and is very good for smaller projects.  
I suspect that the Unix based programs will be better for a larger project 
(180kb) we have since you can adjust the stringency so low. We have used the 
phrap/phred program once and found more and/or bigger contigs than with the 
sequencher. The Unix system seems a pain to me but probably worth the pain of 
learning it. Haven't tried the Staden. 

From:  Christiane Robbins

I personally use sequencher myself and found it much better then
DNA Star. At this point in time though there really isn't a software
package out there that is perfect. Some have better parts then others
and vice versa.
I use sequencher for contiging clones anywhere from 3.5 Kb to 9 Kb.
Sequencher makes it very easy to assemble and then look
at each trace simultaneously  which is great when there is a miscall for a
certain base.
One can also see the protein sequence inthe same contig-nucleotide seq.
frame, as well as the open reading frames. The software doesn't allow
you to open more then one projetc at a given time though. This was a
pain to me when I was sequencing several clones of a larger fragment.

From: Gabriel Dorado 

That's an easy one. Sequencher is by far the best package money can buy. At
least for the moment...

From: "Lassner"  

We are verry happy with sequencher.  Compared to the ABI software, there is
no contest.  It assembles sequences very quickly, even on older 68040 MACs. 
The editing capabilities are also most excellent allowing easy viewing of
ambiguous nucleotides in all sequencing runs.

From: Naomi Thomson

I must admit that I am biased in that i have only
used Sequencher, but I absolutely love it. I run a core for a small
group (130 investigators 50% of whom sequence). We run on average
800 sequencing reactions per month. The majority of the contigs
that we assemble are between 1-3KB; however, we have worked with 
projects of 150 kb. 

We use Sequencher in several ways:

1. All of our sequence files are baked up as projects in Sequencher
Files. We do this in addition to backing up our results file. The advantage
of the sequencher back up is that it allows us to organize our files
by user, which supplements our gel file index, and Sequencher compressess
the files to a much more managable size.

2. All of our contigs are assembled in Sequencher. The variety of views, 
overview, base, summary, restriction map, the translations and ORFs have
all aided in evaluating the sequence data. Also the ease of importing and 
exporting sequences to the variouse blast sites has facilitated proofreading
new sequence.

3. We also use sequencher file as a means of distributing the data from
the core facility to all of our users. We ran a course on Sequencher
for our clients. The course lasted two hours. After which everyone was
competent enough to run on their own. Whenever people do get stuck
help is only a phone call away. The technical support has been 
very friendly and useful.

As I said before I am biased. I would be interested in what
youlearn from the other users. if there is anything out there
that is as good as Sequencher, i would love to try it.


From: Don Seto  

I have used Sequencher, at several different places with very different 
projects.  This program is very useful, simple-to-use, and 
well-supported.  Being Mac-based and networked, it is especially useful 
for institutions that do not have a dedicated computer support staff.  
For ex., in a pharmaceutical setting, over seventy-five different 
researchers, with different needs and backgrounds, were able to use 
Sequencher to analyze DNA sequences retrieved form a core facility (with 
little training).  I've used this program to assemble cosmid-, plasmid-, 
and gene-sized projects, as well as to align few sequences.  Again, 
GeneCodes is very receptive to suggestions and will respond to questions 
and problems.



I highly recommend sequencher for small-scale autosequencing.  Our core
facility converted to automated sequencing a little over a year ago.  We have a
pool of about 60 customers. The majority of our customers only use the core
facility occasionally but they all have converted to sequencher.  We have keyed
copies of sequencher which can be accessed through a server.  Sequencher is
user friendly and versatile.  It is also very fast for assembly. You will find
that Gene Codes provides excellent technical support for sequencher. They are
very accommodating and will add features to their software to suit your needs.

From: Scottie Adams  

Don - I am only familiar with Sequencher, but as a member of the ABRF
DNA Sequencing Committee, we used Sequencher to compare and analyze 73
DNA chromatograms from ABI, ALF and Licor - and it was quite easy to
use and handled the large load gracefully.

From: Stuart M. Brown  

I used Sequencher for two years and loved it.

From:  Giacomo Consalez

Sequencher is by far the best sequence assembly software I have ever tried

From: Jeff Harford/Li-cor 

I have not used the Staden and the Phrap/Phred/Consed/etal packages, but I have 
used Sequencher, as well as DNAStar, MacVector, DNASis, and PCGene.  I have 
come to the personal  impressions that the Sequencher software is the best 
package of all of these, offering all the necessities for sequence assembly 
projects.  Not only does it do these, the things which set it apart from the 
others is that it is always anticipating your needs and thoughts, so that most 
every question that you will ponder, or think of is addressed, and the 
interface is extremely organized.  DNAStar would be my second preference of the 
above software packages.  None of the others listed above accept SCF curves, 
which is a big disadvantage in my perspective.  

I have no direct relationship to any of the above software packages besides 
being a user.
-- d.gilbert--biocomputing--indiana u--bloomington--gilbertd at bio.indiana.edu

More information about the Autoseq mailing list

Send comments to us at biosci-help [At] net.bio.net