Software

AmpliconSuite is a set of 10 interoperable open-source tools for analysing focal amplifications, from raw reads to classified, visualised structures. I founded the project and lead its development.

55 large-scale studies39 by other groups50,626 samples analysedgithub.com/AmpliconSuite

Tools

ToolWhat it doesRole
AmpliconSuite-pipelineEnd-to-end detection, reconstruction and classification from WGSlead
AmpliconClassifierCalls ecDNA, BFB and other amplification typeslead
AmpliconRepository.orgCommunity-editable database of ecDNA annotationsproject lead
AmpliconArchitectBreakpoint graphs of amplified regions from short readsmaintainer
AmpliconReconstructorJoins NGS and optical maps to resolve full structureslead
CoRALecDNA reconstruction from long readsco-developer
CycleVizCircular and linear structure visualizationlead
FaNDOMFast optical genome map alignmentco-lead
ecSimulatorSimulated ecDNA structures for benchmarkinglead
CycleExtractorFast resolution of ecDNA sequence from the breakpoint graphcontributor

Usage

Large-scale studies (50 or more samples) that used AmpliconArchitect or AmpliconSuite, counted by samples analysed and plotted by publication date. Preprints are included. Hover a step to see the study.

Some cohorts were analysed in more than one study.

Large-scale studies using AmpliconSuite tools

Published studies and preprints with 50 or more samples.

DateStudyCohortSamples
Oct 2026Luebeck et al., Nature MethodsCancer cell lines (CCLE)392
Aug 2026ElHarouni et al., NatureHCMI models and tumors989
Jul 2026MacLennan et al., bioRxivCervical cancer (HTMCP)118
Jul 2026Yesudhas et al., bioRxivBladder cancer (TCGA rerun)408
May 2026Chmelova et al., Nature CommunicationsDuctal carcinoma in situ113
Apr 2026Moreno-Rodriguez et al., Genome BiologyProstate cancer (WCDT + CASCADE)193
Mar 2026Nones et al., Genome MedicineSmall cell lung cancer76
Feb 2026Culliford et al., Molecular Cancer ResearchRenal cell carcinoma164
Dec 2025Wong et al., bioRxivGlioblastoma (ecDNA atlas / ecLego3)55
Dec 2025Yu et al., medRxivAcute myeloid leukemia (ATLAS/MEASURE)255
Dec 2025Kim et al., NatureBreast cancer1,364
Dec 2025Pribus et al., bioRxivBreast cancer (ecDNAInspector)231
Oct 2025Hokazono et al., Gastric CancerGastric cancer81
Sep 2025Xiao et al., Cell GenomicsBladder cancer114
Sep 2025Li et al., Cell Stem CellPancreatic organoids260
Aug 2025Kenkre et al., bioRxivPediatric PDX models338
Aug 2025Mout et al., bioRxivProstate cancer69
Jul 2025Khandekar et al., bioRxivLung cancer1,216
Jul 2025Ewing et al., Nature CommunicationsOvarian cancer324
Jun 2025Zhang et al., ResearchSquareTesticular cancer252
Jun 2025Sridhar et al., medRxivPanPedCan3,796
May 2025Akdemir et al., bioRxivGlioma93
May 2025Yost et al., Nature GeneticsPan-cancer 3D genome (TCGA)169
May 2025Kinnersley et al., Nature CommunicationsDiffuse glioma (100kGP)403
Apr 2025Mayr et al., Cancer CellGlioma579
Mar 2025Lv et al., Cancer DiscoveryUrothelial carcinoma1,411
Jan 2025Valle-Inclan et al., CellOsteosarcoma356
Jan 2025Zheng et al., iScienceUrothelial carcinoma199
Nov 2024Bailey et al., NatureGenomics England14,778
Oct 2024Kim et al., Nature GeneticsPan-cancer (TCGA, PCAWG, Hartwig)8,060
Oct 2024O'Neill et al., Cell GenomicsPan-cancer long read (matched WGS)189
Oct 2024Nguyen et al., NatureUrothelial carcinoma71
Aug 2024Lv et al., TheranosticsUrothelial carcinoma80
Aug 2024Nunes et al., NatureColorectal cancer1,063
Aug 2024Cornish et al., NatureColorectal cancer1,761
Aug 2024Fessler et al., NAR CancerCancer cell lines468
Jul 2024Zhang et al., NeoplasiaHematological malignancies208
May 2024Ng et al., Nature CommunicationsEsophageal squamous cell carcinoma710
May 2024Choudhuri et al., Cancer DiscoverySmall cell lung cancer51
Apr 2024Chen et al., Genome MedicineT cell lymphoma71
Feb 2024Wang et al., Nature CommunicationsGCAP Pancancer WES benchmark386
Feb 2024Chen et al., NatureHepatocellular carcinoma (HPV-driven)494
Nov 2023Chapman et al., Nature GeneticsMedulloblastoma481
Oct 2023Rodriguez-Fos et al., Cell GenomicsNeuroblastoma150
Apr 2023Luebeck et al., NatureBarrett's and Esophageal adenocarcinoma286
Apr 2023Pongor et al., Cancer DiscoverySmall cell lung cancer143
Feb 2023Zhong et al., Briefings in BioinformaticseccDNA Atlas319
Oct 2022Cui et al., Nature CommunicationsEsophageal squamous cell carcinoma528
Apr 2022Peng et al., OncogeneeccDNAdb191
Feb 2022Bergstrom et al., NaturePan-cancer (clustered mutations)2,583
Dec 2021Pang et al., Clinical Cancer ResearchHead-and-neck cancer (HPV-driven)72
Nov 2021Zhao et al., Nature CommunicationsGastric cardia adenocarcinoma72
Aug 2020Kim et al., Nature GeneticsPan-cancer (TCGA)3,212
Jan 2019Deshpande et al., Nature CommunicationsAmpliconArchitect paper68
Mar 2017Turner et al., NatureNCI-60113