Open the aru2 contig from your Assembly subfolder to see how the forward and reverse sequences have assembled.
Under the Display tab to the right of the sequence viewer, check the options for calling the consensus sequence. When assembling forward and reverse sequences from the same gene, it makes sense to call the consensus from the sequence of the highest quality at each base, so select Highest Quality under Consensus.
Under the Advanced tab, set Numbering to All sequences. This will display the base numbering from the original sequence reads on each sequence and enable you to see how the two sequences have assembled. You can see that the R sequence is now in the reverse orientation.
Under the Graphs tab, check the Coverage and Identity boxes. The Coverage Graph shows how many sequences the consensus sequence is based on, and the Identity Graph indicates whether the contributing sequences are identical or not. Although you can still see the poor quality sequence which has been annotated as trimmed (pink bars), you can see that the assembler has not used this sequence in calling the consensus sequence or calculating the coverage - only the single good sequence in this region has been used.
For Aru2 there is only a single base where there is a disagreement between the forward and reverse sequences. Zoom in and find this base. You can use the cntrl/command D keyboard shortcut to quickly jump to bases where there are disagreements. At this position the base in the reverse sequence has been called incorrectly - it should be an A but has been called as a C.
You can edit the errant sequence call at this position if you wish, but as we have chosen to call the consensus sequence based on the highest quality the base in the consensus sequence is correct. It is the consensus sequence that is used for downstream analyses so it is not necessary to edit every disagreement in the individual reads if the consensus is correct. Select the Consensus sequence and click Extract. Name your extracted sequence (e.g. aru2 consensus) and click OK.
Now open the ort1 assembly. This sequence has several heterozygous bases annotated which should be checked to ensure they have been called correctly. Click on the first heterozygous annotation on the ort1_R sequence (at base 68 on the consensus) and zoom into 100%. At this base, the single "G" peak has been called correctly so this has been incorrectly identified as a heterozygous base because of a small overlap with the adjacent "C" base. Remove this annotation by right-clicking on it and choosing Annotation→Delete.
Now jump to the next heterozygous base using cntrl/command-D. At this base (position 170 on the Consensus sequence) there is a genuine double peak in both the forward and reverse reads where a C and a T peak are superimposed on top of each other, indicating that this is a real heterozygous base. The base called in the consensus sequence should be a "Y" indicating that this position contains both C and T nucleotides (see IUPAC Notation).
Now check the remaining heterozygous bases in this assembly and edit the consensus sequence by adding IUPAC ambiguity codes if required to reflect the heterozygous positions. Don't forget to click Allow Editing before attempting to make any changes. Save your changes and choose Yes when asked if you want to apply the changes to the original sequences, then select the consensus sequence and Extract it.
Open each one of the other contigs and check for disagreements between the forward and reverse reads and heterozygote bases. Edit them if required, then extract the consensus sequence for each one.