Best contig/clustering tools?

Talon talon34 at hotmail.com
Fri Jan 22 01:27:31 EST 1999


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:

Staden Package with GAP4
TIGR assembler
SPACE/SPASS type package
Any others I missed? Any good commercial packages besides Pangea?

Our current opinion is Phred/Phrap and Staden, using CAFTools and SEALS as glue.

I appreciate any input. Please respond to the group or to me directly.


Mark Evans

evansm at invitrogen.com

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