MCP server that gives LLM agents Oxford Nanopore QC tools — read, alignment, coverage & variant metrics via nanoq/cramino/mosdepth/samtools/bcftools, plus IGV snapshots.
Quick Install
Copy the config for your editor. Some servers may need additional setup — check the README.
Claude Desktop
Claude Code
Cursor
Add to claude_desktop_config.json:
{
"mcpServers": {
"ont_qc_mcp": {
"command": "uvx",
"args": [
"ont-qc-mcp"
]
}
}
}📋 Copy
Run in terminal:
claude mcp add ont_qc_mcp uvx ont-qc-mcp📋 Copy
Add to .cursor/mcp.json:
{
"mcpServers": {
"ont_qc_mcp": {
"command": "uvx",
"args": [
"ont-qc-mcp"
]
}
}
}📋 Copy
Or install with pip: pip install ont-qc-mcp
README Excerpt
Model Context Protocol server exposing lightweight QC/EDA helpers for Oxford Nanopore FASTQ and BAM/CRAM inputs. The server wraps common CLI tools and returns machine-readable summaries for educational and practical workflows. - FASTQ read-level QC via `nanoq` (read count, length/N50, GC, q-score/length histograms).
Tools (17)
alignment_error_profile_tool alignment_summary_tool coverage_stats_tool env_status filter_reads_fastq_tool header_metadata_tool igv_snapshot_tool qc_alignment_tool qc_bed_tool qc_reads_fastq_tool qc_variants_tool qscore_distribution_bam_tool qscore_distribution_fastq_tool read_length_distribution_bam_tool read_length_distribution_fastq_tool sequencing_summary_tool targeted_coverage_tool