Table 1 Summary of eccDNA analysis pipelines and supported experimental methods
From: Comparative analysis of methodologies for detecting extrachromosomal circular DNA
Pipeline (mode) | Published date | Supported experimental methods | Can identify chimeric eccDNA | eccDNA enrichment status | Read format |
|---|---|---|---|---|---|
AmpliconArchitect8 | 2019 | WGS-SR | Y | Non-enriched | Short-read |
Circle-Map16 | 2019 | Circle-Seq-SR 3SEP-SR | N | Enriched | Short-read |
Circle_finder10 (bwa-mem-samblaster, microDNA.InOne.sh) | 2020 | ATAC-Seq-SR Circle-Seq-SR 3SEP-SR | N | Both | Short-read |
ECCsplorer17 | 2022 | Circle-Seq-SR 3SEP-SR | N | Enriched | Short-read |
ecc_finder18 (asm, map) | 2021 | Circle-Seq-SR 3SEP-SR Circle-Seq-LR 3SEP-LR | Y | Enriched | Short-read Long-read |
eccDNA_RCA_nanopore14 | 2021 | Circle-Seq-LR 3SEP-LR | Y | Enriched | Long-read |
NanoCircle7 | 2022 | Circle-Seq-LR 3SEP-LR | Y | Enriched | Long-read |
CReSIL9 | 2023 | WGS-LR Circle-Seq-LR 3SEP-LR | Y | Both | Long-read |
