Table 2 The details of eccDNA analysis tools
From: Extrachromosomal circular DNA: a new potential role in cancer progression
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 | |
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 | |
EcSeg | It is a tool used to quantify ecDNA in metaphase images. It also has an extension to analyze FISH probes | |
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 | |
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 |