Key Resources.

All the code and data generated in this work are freely available through public portals listed below.

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Deposited data
All original code and data for this paper	This paper	https://doi.org/10.5281/zenodo.6859104
The viroid-like cccRNA detection pipeline	This paper	https://github.com/Benjamin-Lee/vdsearch
Software and algorithms
CD-HIT v4.8.1	98	https://github.com/weizhongli/cdhit
HMMER v3.3.2	88	https://github.com/EddyRivasLab/hmmer
Infernal v1.1.4	46	https://github.com/EddyRivasLab/infernal
python-igraph v0.9.10	99	https://github.com/igraph/python-igraph
scikit-bio v0.5.6	100,101	https://github.com/biocore/scikit-bio
MMseqs2 v13.45111	83	https://github.com/soedinglab/mmseqs2
R v4.2.0	R Foundation for Statistical Computing	https://www.r-project.org
Python v3.8.3	Python Software Foundation	https://www.python.org
Nim v1.6.2	102	https://nim-lang.org
ViennaRNA v2.5.0	84	https://github.com/ViennaRNA/ViennaRNA
SeqKit v2.1.0	103	https://github.com/shenwei356/seqkit
Pandas v1.2.0	104	https://github.com/pandas-dev/pandas/
ggplot2 v3.3.6	105	https://github.com/tidyverse/ggplot2/
orfipy v0.0.4	86	https://github.com/urmi-21/orfipy
fastp v0.20.1	76	https://github.com/OpenGene/fastp
Snakemake v6.10.0	106	https://github.com/snakemake/snakemake
circlize v0.4.15	107	https://github.com/jokergoo/circlize
RNAmotif v3.1.1	82	https://github.com/dacase/rnamotif
rnaSPAdes v3.14.1	77	https://github.com/ablab/spades
MinCED v0.4.2	95	https://github.com/ctSkennerton/minced
IQ-TREE v1.6.12	63	https://github.com/iqtree/iqtree2
CLANS	89	http://protevo.eb.tuebingen.mpg.de/download
Sequence Demarcation Tool (SDT) v1.2	90	https://github.com/brejnev/SDTv1.2
PROMALS3D	91	http://prodata.swmed.edu/PROMALS3D
iTOL v6.5.8	92	https://itol.embl.de
bowtie2 v2.4.2	108	http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
BLAST+ suite	96,97	https://blast.ncbi.nlm.nih.gov/
EMBOSS etandem v6.0.0	94	http://emboss.sourceforge.net