Ecc_finder is a comprehensive tool to detect extrachromosomal circular DNA from short and long read sequencing

Extrachromosomal circular DNA (eccDNA) has been observed in different species for decades, and more and more evidence shows that this special type of DNA molecules may play an important role in rapid adaptation. Therefore, characterizing the full landscape of eccDNA has become critical, and there are several protocols for enriching eccDNA and performing short-read or long-read sequencing. However, there currently are no tools available to specifically identify eccDNA from Nanopore reads. More importantly, the current tools based on Illumina short reads lack an efficient standardized pipeline, do not consider repeated loci and cannot be applied to very large genomes. Here we introduce a comprehensive tool to solve both of these two issues (https://github.com/njaupan/ecc_finder). Applying ecc_finder to eccDNA-seq (we named mobilome-seq, Circle-Seq and CIDER-seq uniformly here as eccDNA-seq) data from Arabidopsis, human, and wheat (with genome sizes ranging from 120 Mb to 17 Gb), we document the improvement of computational time, sensitivity, and accuracy and demonstrate its wide applicability and functionality.