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2. To add files go to Traces and click on Add trace files, then select the reads   (.abi files) you want to work with.   3. The program is able to recognize forward and reverse reads from information in the file name if they are properly formatted.  + Go to Traces and click on Find and mark forward/reverse. The default setting looks for \_F for forward and \_R for reverse. This can be edited in the Project settings (you can pull it up by clicking on the picture of the tools at the top of the page) and changing the search strings under trace settings. For an example see Figure  \ref{fig:seqtrace\_1} + If the program is able to recognize the forward/reverse reads it will place an orange left pointing arrow in front of reverse reads and a blue right pointing arrow in front of forward reads. This step is not necessary to get a consensus sequence, it just makes organizing the reads easier.   4. Pull up the Project Settings by clicking on the picture of tools at the top of the page. Click on the Sequence Processing tab, under Sequence trimming unclick the Automatically trim sequence ends button. You should also decrease the Min. confidence score under Consensus settings. The default option is 30 which represents a 99.9% quality score, for many reads this will be too stringent and will not allow you to get enough overlap to create a consensus sequence. A minimum confidence score between 15 and 25 is normally okay but tuning may be required depending on your read quality. For an example see Figure 4. \ref{fig:seqtrace\_2}.  5. Group your forward and reverse reads by highlighting both of them and clicking Group selected forward/reverse files (under Traces)  6. Under Sequences go to Generate Finished Sequences and click on for all trace files. (you will need to redo this every time you change the project settings).  7. To view your consensus sequence, click on the read pair group and then click on the magnifying glass at the top of the page. You should see something like Figure 5. \ref{fig:chromatogram}.  8. The Trace View shows the quality scores, the chromatogram display, and the raw base calls from both the forward and reverse reads, as well as the consensus sequence. The consensus sequence is the middle list of nucleotides. If the program is giving you a string of Ns where your forward and reverse reads do not overlap, you need to decrease the Min confidence score.  9. To export the consensus from the trace view, go to File and click on Export working sequence. This will create a file containing the consensus sequence, which you can upload to BLAST and use to identify the organism.