I've got 454 sequences from a reduce representation library
(restriction enzyme digested, the area from ~600-900 bp was extracted
and used for the 454 without mechanically shearing the DNA)). Hence, I
do not expect that the contigs should be very long and I therefore
used the EST setting when assembling the sequences as to me the
reduced representation data would look similar to EST, and got some
75K contigs (which to me makes sense). However, I also used the genome
setting and got an order of magnitude fewer contigs...
Would anyone know if I'm wrong using the EST settings?