The big picture | Step 1: Setup and validation | What happens | Key options and their impact | Quirks | Step 2: Reading and quality filtering | Step 3: Collapsing identical reads | Key options | Step 4: Assigning reads to experiments | Step 5: Aligning reads to amplicons | Step 6: HDR detection | Step 7: The AlignmentsExperimentSet container | Step 8: Extracting events | Step 9: Filtering artifacts | Step 10: Consensus from both strands | Step 11: Cut-site overlap detection | Step 12: Shifting to relative coordinates | Step 13: Normalization against controls | Step 14: Summarization | Step 15: Reporting | Importing external alignments | Plotting and visualization | Quick reference: parameter summary | Quick reference: pipeline default differences

Why transform through code, not by hand | The 12 required columns | The Amplicon column: case is everything | Strategy A: uppercase the guide plus a buffer (typical) | Strategy B: uppercase the whole interior (for controls or broad analysis) | Summary of buffer interaction | Direction: 0 or 1 | Primers: anchoring sequences, not necessarily PCR primers | What primers do in amplican | Rules for primers | Practical tip | The LLM workflow | Step 1: Export your column headers | Step 2: Prepare the prompt | Step 3: Review and run the generated code | Prompt template | Example: uppercase by guide with buffer | Example: uppercase whole interior (for controls) | Example: detect direction | Example: validate config | Donor extension (advanced) | Validation checklist | Putting it all together

Prerequisites | Quick test with subsampling | Running the full pipeline | Simple one-liner | With custom parameters | Parallel processing | Output folder structure | Reading and interpreting results | config_summary.csv | barcode_reads_filters.csv | Tweak: primer matching | Tweak: which reads to use | Tweak: normalization | When normalization helps | When to disable normalization | How to check if normalization is working correctly | Adjusting the frequency threshold | Tweak: cut buffer | Tweak: PRIMER_DIMER threshold | Tweak: consensus strictness | HDR tweaking | Two detection modes | Decision tree | donor_mismatch behaves differently in each mode | Interaction with cut_buffer | How to check HDR results | Adding a custom HDR percentage column | Iteration workflow | Name folders by parameters | Subsample first, then run full | Compare across runs | Always check RunParameters.txt | Quick reference: tweak decision tree

Description | Amplicon Summary | Amplicon groups | Read distribution | Filtered Reads | Edit rates | Frameshift | Alignments plots

Description | ID Summary | Read distribution | Filtered reads | Edit rates | Frameshift | Alignments plots

Description | Barcode Summary | Groups IDs | Read distribution | Filtered Reads | Edit rates | Frameshift

Description | Group Summary | Read distribution | Filtered reads | Edit rates | Frameshift | Alignments plots

Description | guideRNA Summary | Read distribution | Filtered Reads | Edit rates | Frameshift | Alignments plots

Introduction | Configuration file | Default options | Files created during analysis | barcode_reads_filters.csv | config_summary.csv | RunParameters.txt | "alignments" folder | reports folder | Detailed analysis | Aligning reads | Normalization | Making reports | Plotting alignments events

Explanation of variables | Total reads | Read Quality | Read assignment | Edits | Reads by barcode | Summary Table

Can ampliCan be used for TALENs, NICKASE or other types of genome editing? | I have one control that I want to use for many guides? How should I design the config file? | What is unique reads? | Why are Reads_Edited different from the sum of Reads_Del and Reads_Ins? | Can amplican handle ABI files? | When should I adjust the cutoff for normalization? | What when I have not used unique dual indexing pooling combinations?