Language

English

Publication Date

2-1-2026

Journal

Microbial Genomics

DOI

10.1099/mgen.0.001632

PMID

41642221

PMCID

PMC12877143

PubMedCentral® Posted Date

2-5-2026

PubMedCentral® Full Text Version

Post-print

Abstract

ssDNA viruses are important components of diverse ecosystems; however, it remains challenging to systematically identify and classify them. This is partly due to their broad host range and resulting genomic diversity, structure and rapid evolutionary rates. In addition, distinguishing genuine ssDNA genomes from contaminating sequences in metagenomic datasets (e.g. from commercial kits) has been an unresolved issue for years. Here, we present CRESSENT (CRESS-DNA Extended aNnotation Toolkit), a comprehensive and modular bioinformatic pipeline focused on ssDNA virus 'genome-to-analysis' and annotation. The pipeline integrates multiple functionalities organized into several modules: sequence dereplication, decontamination, phylogenetic analysis, motif discovery, stem-loop structure prediction and recombination detection. Each module can be used independently or in combination with others, allowing researchers to customize their analysis workflow. With this tool, researchers can comprehensively and systematically include ssDNA viruses in their viromics workflows and facilitate comparative genomic studies, which are often limited to dsDNA viruses, therefore leaving behind a crucial component of the microbiome community under study. Benchmarking analyses demonstrated that CRESSENT efficiently processes ssDNA virus datasets of varying scales, completing small family-level analyses within minutes and moderate comparative genomics studies within hours using standard computing resources. Its modular, parallelized design ensures scalability and low memory usage, making it accessible to research groups with diverse computational capacities.

Keywords

Computational Biology, DNA, Single-Stranded, DNA Viruses, annotation, genomics, metagenomics, phylogenetic analysis, ssDNA, ssDNA virus, Genome, Viral, Phylogeny, Molecular Sequence Annotation, Software, Metagenomics, DNA, Viral

Published Open-Access

yes

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