Table 2.

The bioinformatic methods and their functions for analyzing eccDNAs

Bioinformatic methods	Function	Long-read or short-read
AmpliconArchitect [36]	Predicting eccDNAs with 83% sensitivity and 85% precision from short-read WGS data	Short
AmpliconReconstructor [137]	Improving the resolution of large-sized eccDNAs (> 150 kb) in NGS data	Short
Circle-Map [138]	Detecting eccDNAs from Circle-Seq data using split reads and discordant read pairs	Short
Circle-Map + + [43]	Detecting eccDNAs from Circle-Seq data using soft-clipped reads and discordant read pairs with higher efficiency and detection accuracy	Short
Circle_finder [139]	Identifying eccDNAs in bidirectional sequencing data for short-read ATAC-seq, WGS, and WES	Short
ECCsplorer [140]	Detecting candidate eccDNAs from eccDNA-rich data	Short
ecc_finder [141]	Identifying eccDNAs from short-read and long-read sequencing profiles without reliance on copy number information	Long and short
eccDNA_RCA_nanopore [78]	Detecting eccDNAs from Circle-Seq data using Nanopore sequencing	Long
Nanocircle [94]	Detecting eccDNAs from Circle-Seq data using Nanopore sequencing	Long
CReSIL [122]	Utilizing coverage depths and breakpoint reads to identify eccDNAs from long-read WGS data	Long