Error type

Errors can be introduced to sequenced molecules in multiple stages during sequencing experiments. Typically, the primary stages where errors typically occur include PCR amplification, sequencing, and bead synthesis. Inaccuracies are

• Substitution errors:

  • Incorrectly identifying one nucleotide as another.
  • Mistakes made by DNA polymerase during amplification (PCR).
  • Base calling failure (sequencing)

• Insertion errors: Adding extra nucleotides that are not present in the original sequence.

• Deletion errors: Deleting nucleotides that are present in the original sequence.

To simulate reads as more genuinely as possible, Tresor contains a function to allow any types of errors to bo added during PCR amplification, sequencing, and bead synthesis. Users can pass certain values on to the following attributes. Then, Tresor will dispose of the error-adding process.

1. Bead synthesis

   # substitution error
   bead_mutation=True, # True False
   bead_mut_rate=1e-4, # 0.016 0.00004
   # deletion
   bead_deletion=True, # True False
   bead_del_rate=0.1,  # 0.016 0.00004, 2.4e-7
   # insertion
   bead_insertion=True, # True False
   bead_ins_rate=7.1e-7,  # 0.011 0.00001, 7.1e-7
   

2. PCR

   # substitution error
   pcr_err=0.00001
   # deletion
   pcr_deletion=True, # False True
   pcr_del_rate=2.4 * 10e-6,
   # insertion
   pcr_insertion=True, # False True
   pcr_ins_rate=7.1 * 10e-7,
   

3. Sequencing

   # substitution error
   seq_err=0.001,
   # deletion
   seq_deletion=True, # False True
   seq_del_rate=2.4 * 10e-6,
   # insertion
   seq_insertion=True, # False True
   seq_ins_rate=7.1 * 10e-7,