Table 3.

Descriptions and limitations of sequencing-based methods for ecDNA or microDNA construction.

Method	Description	Advantage or limitation	Ref.
AmpliconArchitect	●Superior performance in detecting circular amplicons and complex ecDNAs.	●May generate multiple possible reconstructions in cases where the graph contains duplicated segments.	[8], [36]
AmpliconReconstructor	●Achieve more specific reconstructions of focal amplification, utilizing long-range sequence information that spans and disambiguates multiple junctions.	●Based on breakpoint graphs output by AA.	[38], [43]
HolistIC	●To resolve the difficulty of distinguishing an ecDNA with many amplicons from multiple ecDNAs with overlapping amplicons.	●Requires ecDNA predictions and Hi-C interactions from other tools.	[39]
Circle-Map	●Currently the most commonly used tool for detecting microDNA from Circle-seq data. Can detect repetitive circular DNA.	●Cannot determine variations within DNA circles.	[60]
Circle_finder	●Can utilize traditional ATAC-seq data based on Tn5 library preparations.	●If circles are not enriched, an ATAC-seq read length ≥ 75 bp is necessary to detect chimeric reads, which restricts its broad applicability. Demands high depths.	[61]
ECCsplorer	●Can detect circular DNA by comparison with controls. Can be used for nonmodel organisms.	●Suggest splitting the dataset and performing multiple runs.	[62]
ecc_finder	●Can be applied to nonmodel organisms and giant genomes. Compatible with short-read and nanopore long-read data.	●The great demand for memory.	[63], [64]
CIDER-Seq2	●A custom data analysis package for CIDER-Seq. Primarily used to obtain intact circular virus genomes, enables direct full-length sequencing of eccDNAs less than 10 kb in eukaryotic cells.	●To ensure high accuracy, sequenced circular DNA should preferably be smaller than 10 kb.	[65]
eccDNA_RCA_nanopore	●Strictly based on concatemeric tandem copies (CTC) reads.	●The redundancy of results should be reduced. Ignore eccDNAs that suffer incomplete amplification or DNA breakage events.	[19], [64]
CReSIL	●Enables de novo assemblies of eccDNAs, derived from repetitive regions or consisting of multiple fragments. Can be applied to whole-genome long-read sequencing (WGLS) data.	●Requires high sequence coverage.	[64]