AmpliconSuite

All

17 repositories

AmpliconRepository
Public
Website to host AmpliconSuite outputs, including AA outputs and resulting focal amplification classifications, such as ecDNA.
cancer genomics-data bfb ecdna
HTML
•
BSD 3-Clause "New" or "Revised" License
•5•4•12•1•Updated Aug 15, 2025Aug 15, 2025
ec3D
Public
Reconstruct the three-dimensional structure of extrachromosomal DNA
Python
•
BSD 3-Clause "New" or "Revised" License
•0•6•0•0•Updated Aug 8, 2025Aug 8, 2025
CoRAL
Public
Reconstruction of focal amplifications with long reads
Python
•
BSD 3-Clause "New" or "Revised" License
•5•21•14•2•Updated Jul 22, 2025Jul 22, 2025
AmpliconSuiteAggregator
Public
Aggregates the results from AmpliconSuite for upload to AmpliconRepository.org
Python
•
Other
•4•2•2•0•Updated Jul 17, 2025Jul 17, 2025
AmpliconClassifier
Public
Classify output of AmpliconArchitect to detect types of focal amplifications present
focal double-minutes bfb ecdna ampliconarchitect python-library amplicons
Python
•
BSD 2-Clause "Simplified" License
•11•20•12•0•Updated Jul 11, 2025Jul 11, 2025
AmpliconSuite-pipeline
Public
A quickstart tool for AmpliconArchitect. Performs all preliminary steps (alignment, CNV calling, seed interval detection) required prior to running AmpliconArchitect. Previously called PrepareAA.
cancer cancer-genomics ecdna
Python
•
Other
•29•68•29•0•Updated Jul 3, 2025Jul 3, 2025
EC-comparator
Public
Compare amplicon sets across technologies and methods
Python
•0•1•0•0•Updated Jun 15, 2025Jun 15, 2025
bioconda-recipes
Public
Conda recipes for the bioconda channel.
Shell
•
MIT License
•3.6k•0•0•0•Updated Jun 13, 2025Jun 13, 2025
AmpliconArchitect
Public
Identify one or more connected, focally amplified genomic regions to elucidate the architecture of focal amplifications such as ecDNA.
bioinformatics cancer copynumber ecdna
Python
•
Other
•44•9•0•0•Updated Jun 7, 2025Jun 7, 2025
ecSimulator
Public
Simulate ecDNA structures with user-specified properties.
bioinformatics genome simulation cancer-genomics structural-variation ecdna
Python
•3•1•0•0•Updated Apr 14, 2025Apr 14, 2025
BFBSimulator
Public
Generate sequencing data for simulated breakage-fusion-bridge cycles
MIT License
•0•0•0•0•Updated Mar 12, 2025Mar 12, 2025
CycleViz
Public
Visualize outputs of AmpliconArchitect and AmpliconReconstructor in Circos-style images.
Python
•
GNU General Public License v3.0
•6•25•3•0•Updated Jan 15, 2025Jan 15, 2025
CRISPRCATCH
Public
Pipeline for reconstructing ecDNA based on data from PFGE
Python
•1•0•0•0•Updated Aug 19, 2024Aug 19, 2024
.github
Public
Organization documentation
0•0•0•0•Updated Apr 26, 2024Apr 26, 2024
GenePatternFileDownloader
Public
Utility script for downloading bam (or other file types) from GenePattern
Python
•0•0•0•0•Updated Jan 12, 2024Jan 12, 2024
AmpliconRepository-docs
Public
0•0•0•0•Updated Dec 11, 2023Dec 11, 2023
AmpliconReconstructorOM
Public
Reconstructs complex variation using Bionano optical mapping data and breakpoint graph data
cancer-genomics genome-sequencing genome-analysis genome-assembly optical-mapping bionano ecdna python ngs
Python
•
Other
•6•18•4•0•Updated Nov 13, 2023Nov 13, 2023