nanopolish

nanopolish analyzes nanopore sequencing current signals to detect 5-methylcytosine (5-mC) modifications and genetic variation from Oxford Nanopore Technologies MinION data for epigenetic and genomic analysis.

Key Features:

• Detection of Cytosine Methylations: Quantifies the impact of base modifications on electrical current signals to identify 5-methylcytosine (5-mC) in nanopore data.
• Genetic Variant Detection: Identifies genetic variations from nanopore sequencing reads alongside methylation information.
• HMM Training with Synthetic DNA: Trains a hidden Markov model (HMM) using synthetically methylated DNA to distinguish 5-mC from unmethylated cytosine.
• Raw Signal-Level Analysis: Operates on electrolytic current signal data produced by the Oxford Nanopore Technologies MinION.
• Methylome Sequencing of Human DNA: Enables methylome sequencing of human DNA without requiring specialized library preparation steps.

Scientific Applications:

• Epigenetic Research: Maps cytosine methylation patterns to support studies of gene regulation, development, and disease mechanisms.
• Genomic Studies: Integrates methylation and genetic variation detection for comprehensive genomic analyses.

Methodology:

Performs signal-level analysis of MinION current traces and uses a hidden Markov model (HMM) trained on synthetically methylated DNA to model electrical signal differences caused by 5-methylcytosine (5-mC).