text: user11905: I am analyzing Sanger sequencing data to verify whether or not the correct protein coding sequence was inserted during cloning.
  For each sample, I have both forward and reverse Sanger sequencing reads that cover the coding sequence.
  Would it be better if I first align the forward and reverse reads to get a consensus, and then align the consensus to the reference?
  Or should I just align each read directly to the reference?
  
  user2108: Align all reads from a sample at the same time IMO. This will give you all of the information at once, and it should not be difficult. It should be very obvious whenever there's a disagreement between reads or between reads and reference.
  I would also recommend inspecting chromatograms directly at all sites of interest (such disagreements, insertion sites, possible errors or mutations).
  
original_text: 11905: <p>I am analyzing Sanger sequencing data to verify whether or not the correct protein coding sequence was inserted during cloning.</p>
  <p>For each sample, I have both forward and reverse Sanger sequencing reads that cover the coding sequence.</p>
  <p>Would it be better if I first align the forward and reverse reads to get a consensus, and then align the consensus to the reference?
  Or should I just align each read directly to the reference?</p>
   2108: <p>Align all reads from a sample at the same time IMO. This will give you all of the information at once, and it should not be difficult. It should be very obvious whenever there's a disagreement between reads or between reads and reference.</p>
  <p>I would also recommend inspecting chromatograms directly at all sites of interest (such disagreements, insertion sites, possible errors or mutations).</p>
  