Table 2.

The details of eccDNA analysis tools

Name	Characteristics	Website
AmpliconArchitect	It is a tool which can reconstruct the structure of focally amplified regions in a cancer sample using whole genome sequence short paired-end data	https://github.com/virajbdeshpande/AmpliconArchitect
AmpliconReconstructor	It produces an ordering and orientation of graph segments, with fine-structure information from the breakpoint graph embedded into the large-scale reconstructions and as output, it reports large-scale reconstructions of fCNA amplicons	https://github.com/jluebeck/AmpliconReconstructor
EcSeg	It is a tool used to quantify ecDNA in metaphase images. It also has an extension to analyze FISH probes	https://github.com/ucrajkumar/ecseg
ViFi	It is a tool for detecting viral integration and fusion mRNA sequences from Next Generation Sequencing data. It uses both reference-based read mapping and a phylogenetic-based approach to identify viral reads and incorporates mappability scores of the reads to filter out false positive integration detection	https://github.com/namphuon/ViFi
ECdetect	It performs image pre-segmentation to distinguish between chromosomal and non-chromosomal structures, and calculates the interest (ROI) of the search area of ecDNA. The output of the software includes the original image covered with ecDNA detection, the number of ecDNA found, and their coordinates in the image	ECdetect will be available upon request