If assembling Sanger and 454 data together:
•Enter both Sanger and 454 data at the same time.
•It is not recommended to assemble contigs with contigs.
•Starting with a high stringency setting for the Minimum Match Percentage (85) and then adding the sequences that did not go in using a decreased percentage (80) can be effective.
•If you have a complete Sanger assembly that you are confident with and you are using 454 reads to fill in areas of light coverage, or vice versa, you can use an iterative approach starting with the more complete data set. If you use the iterative approach, turn off Repeat Handling for the second run.
•It is extremely important not to forget to perform vector trimming on the Sanger sequences!