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Fig. 2 | BMC Bioinformatics

Fig. 2

From: ECCsplorer: a pipeline to detect extrachromosomal circular DNA (eccDNA) from next-generation sequencing data

Fig. 2

Outputs of ECCsplorer for different case studies representing the running modes and input data configurations. a–c An ECCsplorer run using A. thaliana circSeq (epi12) and control data (WT) [12] detected EVD/ATCOPIA93 as key eccDNA candidate (orange). a A mapping against the reference genome sequence (TAIR10) revealed eight eccDNA candidate regions. These were identified by applying three criteria: the region is flanked by split reads (at least five), contains discordant mapping reads (at least one pair), and shows a high coverage compared to its neighboring regions (peak prominence of at least one). b The comparative read clustering identified 41.04% of the clustered epi12 reads as potential eccDNA candidates. c To report eccDNA candidates with high confidence the outputs of the mapping and clustering strategies are compared by the ECCsplorer pipeline. The comparative module links the EVD/ATCOPIA93 candidate region from the mapping module to four clusters from the clustering module. d An ECCsplorer run using H. sapiens circSeq data [32] detected one eccDNA candidate region containing genic content (light blue) and many candidate region with low confidence (grey blue). e ECCsplorer analysis using B. vulgaris circSeq data and available sequenceing data [30] as control data detected multiple candidate clusters that were in the following annotated as mitchondrial minicircles a/d/pO (orange). f Overview on the running modes, their required input data and the corresponding case studies

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