Logo DT4DDS

Challenge submission

A valid submission name is required.
Choose a name for your submission.
Please provide a valid set of oligo sequences. They may only contain A, C, G, and T. At most 10000 sequences with up to 150 nucleotides each are allowed.
#oligos 0
max. length 0
avg. GC 0%
Random
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Provide the oligo sequences for simulation. Enter each oligo on its own line. Limited to 10000 oligos of max. 150 nt each.
A valid challenge is required.
Select the challenge for simulation. More details below.

Recovery of oligo fragments after long-term storage, assuming the very low error rates from state-of-the-art commercial synthesis and high-fidelity PCR, but at very low physical coverage and oligo breakage equivalent to around five half-lives of storage. In addition, the sequencing depth is low, and the sequencing data is biased against short oligo fragments.
  • 0.0007 deletions per nt, 0.0049 substitutions per nt, and no insertions
  • 0.023 breakages per nt, biased towards G and A
  • 10x physical coverage, 30x sequencing depth
  • Presence of a random CT-tail at the end of sequencing reads from sequencing preparation

Application of photolithographic synthesis in a DNA-of-things context, assuming errors representative of photolithographic synthesis with a high physical coverage and sequencing depth. In addition, the beginning and end of each sequence are randomly truncated.
  • 0.075 deletions per nt, 0.012 insertions per nt, and 0.025 substitutions per nt
  • 200x physical coverage, 50x sequencing depth
  • Both oligo ends randomly truncated

Error profile

Estimated from challenge
  • Substitutions
    overall per nt
    1.2%
  • Deletions
    overall per nt
    1.2%
  • Insertions
    overall per nt
    0.0%
  • Coverage bias
    overall
    0.53