A method for circular DNA detection based on probabilistic mapping of ultrashort reads

A quickstart tool for AmpliconArchitect. Performs all preliminary steps (alignment, CNV calling, seed interval detection) required prior to running AmpliconArchitect. Previously called PrepareAA.

Pipeline for the identification of extrachromosomal circular DNA (ecDNA) from Circle-seq, WGS, and ATAC-seq data that were generated from cancer and other eukaryotic cells.

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

GCAP (Gene-level Circular Amplicon Prediction) firstly implements extrachromosomal DNA detection from whole-exome-sequencing (WES) data and absolute copy number profiles. https://shixiangwang.r-universe.dev/gcap

Tool used to quantify extrachromosomal DNA (ecDNA) in metaphase images stained with DAPI and FISH probes.

Classify output of AmpliconArchitect to detect types of focal amplifications present

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

ecc_caller is a pipeline designed to take Illumina NovaSeq paired end sequencing reads generated from isolated circular DNA and call eccDNA forming regions.

Visualize circular ecDNA reconstructions using Decoil-viz

Scripts and analysis for the Giurgiu et al. 2024. Genome Research. "Reconstructing extrachromosomal DNA structural heterogeneity from long-read sequencing data using Decoil".

Wraps the AmpliconSuite-pipeline workflow to identify one or more connected genomic regions which have copy number amplifications.

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

Simulate ecDNA structures with user-specified properties.

Simulation of ecDNA sequence templates

Evolutionary models of extrachromosomal DNA (ecDNA).