I need to find consensus sequence between 6 genomes, each of them with more than 5mb of base pairs. I am using Genious software, I have selected the Align/ Assemble map to References option and the following parameters: Mapper: Geneious, Sensitivity: Custom sensibility, Fine Tuning: Iterate uo to 5 times, Do not trim, {Reads Name} assembled to {Reference Name}, Save assembly report, Save contigs, Save consensus sequences. Options. Thereshold: Highest Quality (75%), Theresold for sequences without quality 65%, Assign Quality: Total, If no coverage call Ref, Split into separate sequences around "?" calls, Allow Gaps, Max Per Read 30%, Word Length: 14, Ignore words repeated more than 20 times, Maximum Mismatches Per Read: 30%, Accurately map reads with errors to repeat regions, Max Gap Size: 1,000, Index Word Lenght 12, Maximum Ambiguity: 4. The result is a sequence with multiple bases on "?". How do I generate consensus sequence? What parameters do I need to fix?
Since
Geneiousis commercial software you may want to reach out to their tech support. While you may get an answer here not many are likely to have access to this software.