It would be really helpful if there was an option to trim the first X and last Y bases as this would really help remove the junk that Sanger seq end up having here, leading to fewer ambiguous bases in the resulting consensus. For example in COI barcoding I find trimming each sequence to 650bp and then trimming the first 100bp before assembly removes 99% of the issues. Assembling the two 550bp sequences still results in a 650bp contig, but with far fewer Ns and clean sequence across the contig, admittedly with 100bp overhangs.
It would be really helpful if there was an option to trim the first X and last Y bases as this would really help remove the junk that Sanger seq end up having here, leading to fewer ambiguous bases in the resulting consensus. For example in COI barcoding I find trimming each sequence to 650bp and then trimming the first 100bp before assembly removes 99% of the issues. Assembling the two 550bp sequences still results in a 650bp contig, but with far fewer Ns and clean sequence across the contig, admittedly with 100bp overhangs.