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
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.
evansm at invitrogen.com