Repositories list

• CycleExtractor

  Public
  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 22, 2026Apr 22, 2026

• EC-comparator

  Public
  Compare amplicon sets across technologies and methods

  Python

  •00 forks•11 star•00 issues•00 pull requests•Updated Apr 22, 2026Apr 22, 2026

• BFBArchitect

  Public
  A tool for reconstructing BFB with long reads

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •00 forks•22 stars•00 issues•00 pull requests•Updated Apr 20, 2026Apr 20, 2026

• AmpliconRepository

  Public
  Website to host AmpliconSuite outputs, including AA outputs and resulting focal amplification classifications, such as ecDNA.

  cancergenomics-databfb+ 1

  cancergenomics-databfbecdna

  HTML

  •

  BSD 3-Clause "New" or "Revised" License

  •55 forks•55 stars•1818 issues•00 pull requests•Updated Apr 20, 2026Apr 20, 2026

• CoRAL

  Public
  CoRAL: Reconstruction of focal amplifications with long reads

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •99 forks•2424 stars•1717 issues•44 pull requests•Updated Apr 16, 2026Apr 16, 2026

• AmpliconSuite-pipeline

  Public
  A quickstart tool for AmpliconArchitect. Enables all steps (alignment, CNV calling, seed interval detection) prior to running AmpliconArchitect, and invokes Amp…

  cancercancer-genomicsecdna

  cancercancer-genomicsecdna

  Python

  •

  Other

  •3232 forks•8080 stars•3434 issues•00 pull requests•Updated Apr 8, 2026Apr 8, 2026

• AmpliconArchitect

  Public
  Identify one or more connected, focally amplified genomic regions to elucidate the architecture of focal amplifications such as ecDNA.

  bioinformaticscancercopynumber+ 1

  bioinformaticscancercopynumberecdna

  Python

  •

  Other

  •4343 forks•1010 stars•00 issues•00 pull requests•Updated Apr 8, 2026Apr 8, 2026

• bioconda-recipes

  Public
  Conda recipes for the bioconda channel.

  Shell

  •

  MIT License

  •3.9k3.9k forks•00 stars•00 issues•00 pull requests•Updated Mar 19, 2026Mar 19, 2026

• AmpliconClassifier

  Public
  Classify output of AmpliconArchitect to detect types of focal amplifications present

  python-libraryampliconsfocal+ 4

  python-libraryampliconsfocaldouble-minutesbfbecdnaampliconarchitect

  Python

  •

  BSD 2-Clause "Simplified" License

  •1111 forks•2121 stars•1515 issues•00 pull requests•Updated Mar 19, 2026Mar 19, 2026

• AmpliconSuiteAggregator

  Public
  Aggregates the results from AmpliconSuite for upload to AmpliconRepository.org

  Python

  •

  Other

  •44 forks•22 stars•22 issues•00 pull requests•Updated Mar 14, 2026Mar 14, 2026

• ecSimulator

  Public
  Simulate ecDNA structures with user-specified properties.

  bioinformaticsgenomesimulation+ 3

  bioinformaticsgenomesimulationcancer-genomicsstructural-variationecdna

  Python

  •33 forks•33 stars•00 issues•00 pull requests•Updated Feb 10, 2026Feb 10, 2026

• AmpliconRepository-docs

  Public
  00 forks•00 stars•00 issues•00 pull requests•Updated Feb 9, 2026Feb 9, 2026

• CycleViz

  Public
  Visualize outputs of AmpliconArchitect and AmpliconReconstructor in Circos-style images.

  Python

  •

  GNU General Public License v3.0

  •66 forks•2929 stars•44 issues•00 pull requests•Updated Oct 10, 2025Oct 10, 2025

• ec3D

  Public
  Reconstruct the three-dimensional structure of extrachromosomal DNA

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •00 forks•1010 stars•00 issues•11 pull request•Updated Sep 15, 2025Sep 15, 2025

• BFBSimulator

  Public
  Generate sequencing data for simulated breakage-fusion-bridge cycles

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 12, 2025Mar 12, 2025

• CRISPRCATCH

  Public
  Pipeline for reconstructing ecDNA based on data from PFGE

  Python

  •11 fork•00 stars•00 issues•00 pull requests•Updated Aug 19, 2024Aug 19, 2024

• .github

  Public
  Organization documentation

  00 forks•00 stars•00 issues•00 pull requests•Updated Apr 26, 2024Apr 26, 2024

• GenePatternFileDownloader

  Public
  Utility script for downloading bam (or other file types) from GenePattern

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 12, 2024Jan 12, 2024

• AmpliconReconstructorOM

  Public
  Reconstructs complex variation using Bionano optical mapping data and breakpoint graph data

  pythonngscancer-genomics+ 6

  pythonngscancer-genomicsgenome-sequencinggenome-analysisgenome-assemblyoptical-mappingbionanoecdna

  Python

  •

  Other

  •66 forks•1919 stars•55 issues•00 pull requests•Updated Nov 13, 2023Nov 13, 2023