circdna
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.
circle-map
A method for circular DNA detection based on probabilistic mapping of ultrashort reads
https://github.com/ampliconsuite/ampliconclassifier
Classify output of AmpliconArchitect to detect types of focal amplifications present
https://github.com/ampliconsuite/ampliconreconstructorom
Reconstructs complex variation using Bionano optical mapping data and breakpoint graph data
https://github.com/ampliconsuite/ampliconrepository
Website to host AmpliconSuite outputs, including AA outputs and resulting focal amplification classifications, such as ecDNA.
ampliconsuite-pipeline
A quickstart tool for AmpliconArchitect. Performs all preliminary steps (alignment, CNV calling, seed interval detection) required prior to running AmpliconArchitect. Previously called PrepareAA.
https://github.com/ampliconsuite/ampliconarchitect
Identify one or more connected, focally amplified genomic regions to elucidate the architecture of focal amplifications such as ecDNA.
https://github.com/ampliconsuite/ecsimulator
Simulate ecDNA structures with user-specified properties.