I sanger sequenced many reads with primers that I know the correct order. I mapped the reads to the reference sequence using bowtie. I found that Pregap4 and Gap4 have excellent manipulation and visualization of sequences and chromatograms. The only annoying thing is I have to denovo assemble each time as oppose to telling it the correct order/mapping. This sometimes leads to incorrect assemblies that I have to manually fix before polishing the sequences.
For the most part it does seem that if I use low confidence threshold it can assemble better, but then I am left with more low confidence bases to correct in the end. My other thought was I could let it do low confidence assembly but is there an option to do post assembly filtering?