bio-long-read-sequencing-nanopore-methylation
Calls DNA methylation from Oxford Nanopore sequencing data using signal-level analysis. Use when detecting 5mC or 6mA modifications directly from nanopore reads without bisulfite conversion.
npx skills add majiayu000/claude-skill-registry --skill nanopore-methylation --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Nanopore Methylation Calling ## Modern Workflow (modkit) ONT's modkit is the recommended tool for methylation analysis from basecalled data. ### Extract Methylation from BAM ```bash # Assumes BAM has MM/ML tags from dorado basecalling modkit pileup input.bam methylation.bed \ --ref reference.fa \ --cpg \ --combine-strands ``` ### Output Format ``` # bedMethyl format chr1 1000 1001 . 10 + 1000 1001 0,0,0 10 80.5 # Columns: chrom, start, end, name, score, strand, thickStart, thickEnd, # itemRgb, coverage, percent_modified ``` ## Basecalling with Methylation ```bash # Dorado basecalling with 5mC model dorado basecaller dna_r10.4.1_e8.2_400bps_sup@v4.2.0 \ pod5_dir/ \ --modified-bases 5mCG \ > calls.bam # Index and align samtools fastq calls.bam | \ minimap2 -ax map-ont -y reference.fa - | \ samtools sort -o aligned.bam samtools index aligned.bam ``` ## Region-Specific Analysis ```bash # CpG islands only modkit pileup aligned.bam cpg_islands.bed \ --ref reference.fa \ --cpg \ --include-bed cpg_islands.bed # Promoter regions modkit pileup aligned.bam promoters.bed \ --ref reference.fa \ --cpg \ --include-bed promoters.bed ``` ## Sample Summary ```bash # Get modification summary statis
- Modern Workflow (modkit)
- Extract Methylation from BAM
- Output Format
- Basecalling with Methylation
- Region-Specific Analysis
- Sample Summary
- Differential Methylation
- Quality Considerations
- Related Skills
Assumes BAM has MM/ML tags from dorado basecalling modkit pileup input.bam methylation.bed \ Dorado basecalling with 5mC model dorado basecaller dna_r10.4.1_e8.2_400bps_sup@v4.2.0 \ pod5_dir/ \ Index and align samtools fastq calls.bam | \ minimap2 -ax map-ont -y reference.fa - | \ samtools sort -o aligned.bam samtools index aligned.bam
What does the bio-long-read-sequencing-nanopore-methylation skill do?
Calls DNA methylation from Oxford Nanopore sequencing data using signal-level analysis. Use when detecting 5mC or 6mA modifications directly from nanopore reads without bisulfite conversion.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill nanopore-methylation --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From majiayu000/claude-skill-registry, a repository with 534 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.