Optimal results of EST assembly occur when the contigs that are created correspond to full-length transcripts. For larger EST collections, many contigs may be generated, each corresponding to a distinct transcript. If you have genomic sequences, you may be able to assemble a collection of ESTs onto one or more genomic sequence backbones. This reduces the number of contigs in the assembly.
For eukaryotic EST assemblies, you should consider modifying Assembling Parameters to accommodate gaps corresponding to introns. (Also see Optimizing EST assembly parameters.) Note, however, that while such EST-backbone assemblies may be useful for organisms that have short introns, for organisms with large introns it may not be possible to adjust assembly parameters sufficiently to accept the large gaps in the alignments. For larger data sets, like most EST assemblies, it is recommended to use the Pro assembly method. Using the Pro assembler will decrease the amount of time needed to complete your assembly. For more information on the Pro assembler, see Choosing Between the Classic or Pro Assemblers.