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
Package: amplican 1.35.4
Eivind Valen
amplican: Automated analysis of CRISPR experiments
`amplican` performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems.
Authors:
amplican_1.35.4.tar.gz
amplican_1.35.4.zip(r-4.7)amplican_1.35.4.zip(r-4.6)amplican_1.35.4.zip(r-4.5)
amplican_1.35.4.tgz(r-4.6-x86_64)amplican_1.35.4.tgz(r-4.6-arm64)amplican_1.35.4.tgz(r-4.5-x86_64)amplican_1.35.4.tgz(r-4.5-arm64)
amplican_1.35.4.tar.gz(r-4.7-arm64)amplican_1.35.4.tar.gz(r-4.7-x86_64)amplican_1.35.4.tar.gz(r-4.6-arm64)amplican_1.35.4.tar.gz(r-4.6-x86_64)
amplican_1.35.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
amplican/json (API)
| # Install 'amplican' in R: |
| install.packages('amplican', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/valenlab/amplican/issues
On BioConductor:amplican-1.35.1(bioc 3.24)amplican-1.34.0(bioc 3.23)
immunooncologytechnologyalignmentqpcrcrisprcpp
Last updated from:c3ec0014bc. Checks:1 FAILURE, 11 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | FAILURE | 253 | ||
| linux-devel-arm64 | WARNING | 269 | ||
| linux-devel-x86_64 | WARNING | 253 | ||
| source / vignettes | OK | 370 | ||
| linux-release-arm64 | WARNING | 273 | ||
| linux-release-x86_64 | WARNING | 305 | ||
| macos-release-arm64 | WARNING | 224 | ||
| macos-release-x86_64 | WARNING | 537 | ||
| macos-oldrel-arm64 | WARNING | 208 | ||
| macos-oldrel-x86_64 | WARNING | 330 | ||
| windows-devel | WARNING | 270 | ||
| windows-release | WARNING | 251 | ||
| windows-oldrel | WARNING | 256 | ||
| wasm-release | OK | 155 |
Exports:AlignmentsExperimentSetamplican_print_readsamplicanAlignamplicanConsensusamplicanFilteramplicanMapamplicanNormalizeamplicanOverlapamplicanPipelineamplicanPipelineConservativeamplicanReportamplicanSummarizeassignedCountbarcodeDatabarcodeData<-cigarsToEventscomb_alongexperimentDataexperimentData<-extractEventsfindEOPfindLQRfindPDfwdReadsfwdReads<-fwdReadsTypefwdReadsType<-get_seqgetEventsis_hdr_strictlookupAlignmentmetaplot_deletionsmetaplot_insertionsmetaplot_mismatchespairToEventsplot_cutsplot_deletionsplot_heightplot_heterogeneityplot_insertionsplot_mismatchesplot_variantsreadCountsreadCounts<-rveReadsrveReads<-rveReadsTyperveReadsType<-unassignedCountunassignedDataunassignedData<-wafflewriteAlignments
Dependencies:abindbase64encBHBiobaseBiocGenericsBiocParallelBiostringsbitopsbslibcachemcigarillocliclustercodetoolscpp11crayondata.tableDelayedArraydeldirdigestevaluatefarverfastmapfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesggplot2ggthemesgluegridExtragtablehighrhtmltoolshwriterinterpIRangesisobandjpegjquerylibjsonliteknitrlabelinglambda.rlatticelatticeExtralifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimepillarpkgconfigpngpurrrpwalignR6rappdirsRColorBrewerRcppRcppEigenRhtslibrlangrmarkdownRsamtoolsS4ArraysS4VectorsS7sassscalesSeqinfoShortReadsnowSparseArraystringistringrSummarizedExperimenttibbletinytexutf8vctrsviridisLitewithrxfunXVectoryaml
ampliCan Code Explained
Last update: 2026-06-13
Started: 2026-06-13
Preparing amplican config from Excel with LLM assistance
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
Last update: 2026-06-13
Started: 2026-06-13
Tweaking amplican output
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
Last update: 2026-06-13
Started: 2026-06-13
Report breakdown by amplicon sequence
Description | Amplicon Summary | Amplicon groups | Read distribution | Filtered Reads | Edit rates | Frameshift | Alignments plots
Last update: 2026-04-26
Started: 2017-06-02
Report breakdown by ID
Description | ID Summary | Read distribution | Filtered reads | Edit rates | Frameshift | Alignments plots
Last update: 2026-04-26
Started: 2017-06-02
Report breakdown by barcode
Description | Barcode Summary | Groups IDs | Read distribution | Filtered Reads | Edit rates | Frameshift
Last update: 2026-04-01
Started: 2017-06-02
Report breakdown by group
Description | Group Summary | Read distribution | Filtered reads | Edit rates | Frameshift | Alignments plots
Last update: 2026-04-01
Started: 2017-06-02
Report breakdown by guideRNA
Description | guideRNA Summary | Read distribution | Filtered Reads | Edit rates | Frameshift | Alignments plots
Last update: 2026-04-01
Started: 2017-06-02
ampliCan Overview
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
Last update: 2026-03-31
Started: 2016-08-23
Summary Read Report
Explanation of variables | Total reads | Read Quality | Read assignment | Edits | Reads by barcode | Summary Table
Last update: 2025-11-11
Started: 2017-04-20
ampliCan FAQ
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?
Last update: 2023-05-02
Started: 2018-09-14
