nanodisco

nanodisco identifies de novo DNA methylation motifs and methylation types (6-methyladenine (6mA), 5-methylcytosine (5mC), and 4-methylcytosine (4mC)) from nanopore sequencing data for bacterial isolates and microbiomes to enable methylome characterization and methylation-based metagenomic binning.

Key Features:

• De Novo Methylation Motif Discovery: Identifies novel DNA methylation motifs across bacterial species from nanopore sequencing data.
• Methylation Typing and Fine Mapping: Distinguishes 6mA, 5mC, and 4mC and pinpoints which position within a motif is methylated using a multi-label classification framework.
• Metagenomic Binning Using Methylation Patterns: Uses methylation patterns as epigenetic barcodes to construct and cluster a methylation profile matrix for high-resolution metagenomic binning, host association of mobile genetic elements, and detection of misassembled contigs.
• Integration for Comprehensive Analysis: Integrates motif discovery and metagenomic analysis to enable de novo methylation studies from complex microbial communities, including the mouse gut microbiome.

Scientific Applications:

• De novo methylome discovery: Enables discovery of previously unknown bacterial methylomes from isolates and microbiomes.
• Study of cellular defense and gene regulation: Supports investigation of restriction-modification systems, other cellular defense mechanisms, and methylation-linked gene regulation.
• Metagenomic assembly curation and host association: Facilitates association of mobile genetic elements with host genomes and identification of misassembled metagenomic contigs.
• Microbiome epigenomics: Applicable to complex microbial communities such as the mouse gut microbiome for community-level methylation analyses.

Methodology:

Performs de novo motif discovery from nanopore sequencing reads, applies a multi-label classification framework to type 6mA/5mC/4mC and map methylated positions within motifs, and constructs and clusters a methylation profile matrix for metagenomic binning and host association.