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Scenario submission

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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%
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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 scenario is required.
Select the scenario for simulation. More details below.

Scenario inspired by the density benchmark established by Organick et al. (doi:10.1038/nbt.4079) using best-case synthesis and no aging.
  • Synthesis: material deposition-based synthesis, high homogeneity
  • PCR: 30 cycles total with high-fidelity polymerase
  • Sequencing: 6.2x sequencing depth, 150 nt paired-end SBS

Scenario based on the "Density Benchmark Scenario", but including storage for one half-life (about 100 years at 10°C).
  • Synthesis: material deposition-based synthesis, high homogeneity
  • PCR: 30 cycles total with high-fidelity polymerase
  • Aging: one half-life of decay at 6.2x coverage
  • Sequencing: 150 nt paired-end SBS, 50x sequencing depth

Scenario using the lowest-fidelity processes analyzed in the paper, including aging for one half-life (about 100 years at 10°C).
  • Synthesis: electrochemical synthesis, poor homogeneity
  • PCR: 50 cycles total with Taq polymerase and poor efficiency bias
  • Aging: one half-life of decay at 10x coverage
  • Sequencing: 150 nt paired-end SBS, 50x sequencing depth

Scenario focussing on the effects of long storage durations on the oligo coverage. Includes aging for five half-lives (about 500 years at 10°C).
  • Synthesis: electrochemical synthesis, medium homogeneity
  • PCR: 30 cycles total with Taq polymerase and medium efficiency bias
  • Aging: five half-lifes of decay at 100x coverage
  • Sequencing: 150 nt paired-end SBS, 50x sequencing depth

Error profile

Estimated from settings
  • Substitutions
    PCR & Sequencing
    1.2%
  • Deletions
    Synthesis
    1.2%
  • Insertions
    negligible
    0.0%
  • Coverage bias
    Synthesis & PCR
    0.53