Best contig/clustering tools?

Crepineau florent crepinau at sb-roscoff.fr
Tue Jan 26 07:55:45 EST 1999


In article <36AD44AF.18EC1098 at compusmart.ab.ca>, Andrew Gardner
<andrewg at compusmart.ab.ca> wrote:

> > I am trying to decide which software is the best to use. We want to
> > assemble fragments from HTS sequencing (of cDNA's) and then be able to
> > cluster the results with Genbank/Unigene. So I am interested in the
> > opinion of this group. Which do you think is best? My criteria for "best"
> > is 1. accuracy and 2. scriptability (for automation).  The choices are:

  
To assemble, for UNIX I know :
   TIGRassembler that assemble reads in contigs (free)
it is fast and very simple and is also compatible with:
   PhredPhrapConsed that does contig assembly and allows editing of
sequences assembled (free)
it is rather fast but one need to check veracity of assemblies
   Acembly which goes with ACEDB, the database system (free).
I have not been able to use it with my own SCF traces but I am using an
unusual automatic sequencer.

To cluster the results whith Genbank a BLAST may be sufficient. To
automate it you could have a look at MSPcrunch or DBWatcher.
For Unigene maybe you could try to contact them and ask for an access to
the softwares they have developed. Otherwise ACEDB may be a good solution
there was a paper in Genome research (Miller, 1997) where they described
an ACEDB database with IMAGE and UNIGENE as an integrated resources ....

Hope this help

florent




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