Simulation Guides

Task-focused guides for designing simulations. Start with the Experiment builder; the rest are deep dives into specific biological mechanisms or pipeline patterns.

Start here

• The Experiment builder — the control panel. Every pipeline goes through this builder; this is the one guide every user should read.

Biology mechanisms

• Recombination + junction biology — V(D)J join, trim-and-fill, productivity contract.
• Junction N/P additions — N-base composition models, P-nucleotide lengths, layout diagrams.
• D inversion + receptor revision — the two recombination-stage editing mechanisms.
• SHM and mutation targeting — uniform vs S5F, per-segment and per-V-subregion rates, counter partitions.
• Clonal simulation overview — choose between BCR lineage trees, TCR / flat-BCR clone-size repertoires, and legacy fixed-size stars.
• Clonal lineage trees — BCR affinity-maturation trees with SHM, selection, sampling, and ground-truth exports.
• Clonal repertoires — TCR and flat-BCR abundance models with heavy-tailed clone sizes and duplicate_count.

Library + sequencing

• Corruption + sequencing artefacts — PCR errors, sequencing errors, indels, end-loss, N corruption, strand orientation.
• Paired-end reads and FASTQ — R1 / R2 projection + quality models.

Reproducibility

• Trace, replay, reproducibility — what a trace contains, how to replay it, every failure mode.

Cartridge authoring (separate section)

For building or estimating reference cartridges, see the dedicated Reference Cartridge Authoring section.

For higher-level routing by reader intent, see Choose your path.