Agent skill

bio-longread-alignment

Align long reads using minimap2 for Oxford Nanopore and PacBio data. Supports various presets for different read types and applications. Use when aligning ONT or PacBio reads to a reference genome for variant calling, SV detection, or coverage analysis.

View SKILL.md on GitHub Repository
Stars 2,009
Forks 275

Install this agent skill to your Project

npx add-skill https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-longread-alignment

SKILL.md

Version Compatibility

Reference examples tested with: minimap2 2.26+, samtools 1.19+

Before using code patterns, verify installed versions match. If versions differ:

  • CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Long-Read Alignment with minimap2

"Align my long reads to the reference" → Map ONT or PacBio reads using minimap2 with technology-specific presets for optimal sensitivity and accuracy.

  • CLI: minimap2 -ax map-ont ref.fa reads.fq | samtools sort -o aligned.bam (ONT), minimap2 -ax map-hifi (PacBio HiFi)

Oxford Nanopore Alignment

bash
# Basic ONT alignment
minimap2 -ax map-ont reference.fa reads.fastq.gz | \
    samtools sort -o aligned.bam
samtools index aligned.bam

PacBio HiFi Alignment

bash
# PacBio HiFi reads (high accuracy)
minimap2 -ax map-hifi reference.fa reads.fastq.gz | \
    samtools sort -o aligned.bam
samtools index aligned.bam

PacBio CLR Alignment

bash
# PacBio CLR (continuous long reads, lower accuracy)
minimap2 -ax map-pb reference.fa reads.fastq.gz | \
    samtools sort -o aligned.bam
samtools index aligned.bam

Pre-Build Index for Multiple Runs

bash
# Build index once
minimap2 -d reference.mmi reference.fa

# Use index for alignment
minimap2 -ax map-ont reference.mmi reads.fastq.gz | samtools sort -o aligned.bam

Common Options

bash
minimap2 -ax map-ont \
    -t 8 \                         # Threads
    -R '@RG\tID:sample\tSM:sample' \  # Read group
    --secondary=no \               # No secondary alignments
    --MD \                         # Generate MD tag for variants
    -Y \                           # Use soft clipping for supplementary
    reference.fa reads.fastq.gz | \
    samtools sort -@ 4 -o aligned.bam

Splice-Aware Alignment (RNA)

bash
# For direct RNA or cDNA sequencing
minimap2 -ax splice reference.fa reads.fastq.gz | \
    samtools sort -o aligned.bam

With Junction BED (Known Splice Sites)

bash
# Provide known splice junctions
minimap2 -ax splice --junc-bed junctions.bed \
    reference.fa reads.fastq.gz | samtools sort -o aligned.bam

Assembly to Reference Alignment

bash
# Assembly with ~0.1% divergence
minimap2 -ax asm5 reference.fa assembly.fa > aligned.sam

# Assembly with higher divergence (~5%)
minimap2 -ax asm20 reference.fa assembly.fa > aligned.sam

Output PAF (Faster, No BAM)

bash
# PAF format (faster, for quick analysis)
minimap2 -x map-ont reference.fa reads.fastq.gz > alignments.paf

Keep Secondary and Supplementary

bash
# Keep all alignments (for SV calling)
minimap2 -ax map-ont \
    --secondary=yes \
    -N 5 \                         # Max secondary alignments
    reference.fa reads.fastq.gz | samtools sort -o aligned.bam

Filter Alignments

bash
# During alignment pipeline
minimap2 -ax map-ont reference.fa reads.fastq.gz | \
    samtools view -b -q 10 | \     # Min mapping quality 10
    samtools sort -o aligned.bam

Multiple FASTQ Files

bash
# Concatenate inputs
minimap2 -ax map-ont reference.fa reads1.fastq.gz reads2.fastq.gz | \
    samtools sort -o aligned.bam

# Or use file list
cat file_list.txt | xargs minimap2 -ax map-ont reference.fa | \
    samtools sort -o aligned.bam

Output Statistics

bash
# Get alignment statistics
samtools flagstat aligned.bam

# Detailed stats
samtools stats aligned.bam | grep ^SN

Convert PAF to BED

bash
# Extract alignments to BED
awk 'OFS="\t" {print $6, $8, $9, $1, $12, ($5=="+")?"+":"-"}' alignments.paf > alignments.bed

Key Presets

Preset Description Best For
map-ont ONT reads Nanopore genomic
map-hifi PacBio HiFi PacBio genomic
map-pb PacBio CLR PacBio CLR
splice Long RNA reads cDNA, direct RNA
asm5 Low divergence Same species assembly
asm20 High divergence Cross-species assembly
sr Short reads Illumina (basic)

Key Parameters

Parameter Default Description
-t 3 CPU threads
-k 15 K-mer size
-w 10 Minimizer window
-a off Output SAM
-x none Preset
--secondary yes Output secondary
-N 5 Max secondary alignments
--MD off Generate MD tag
-R none Read group header
-Y off Soft clipping for supplementary

Output Formats

Format Flag Description
PAF (default) Pairwise Alignment Format
SAM -a Sequence Alignment Map
BAM -a | samtools Binary SAM

Related Skills

  • medaka-polishing - Polish consensus with medaka
  • structural-variants - Call SVs from alignments
  • alignment-files/sam-bam-basics - BAM manipulation

Recommended Agent Skills

Expand your agent's capabilities with these related and highly-rated skills.

FreedomIntelligence/OpenClaw-Medical-Skills

vcf-annotator

Annotate VCF variants with VEP, ClinVar, gnomAD frequencies, and ancestry-aware context. Generates prioritised variant reports.

2,009 275
Explore
FreedomIntelligence/OpenClaw-Medical-Skills

chemist-analyst

Analyzes events through chemistry lens using molecular structure, reaction mechanisms, thermodynamics, kinetics, and analytical techniques (spectroscopy, chromatography, mass spectrometry). Provides insights on chemical processes, material properties, reaction pathways, synthesis, and analytical methods. Use when: Chemical reactions, material analysis, synthesis planning, process optimization, environmental chemistry. Evaluates: Molecular structure, reaction mechanisms, yield, selectivity, safety, environmental impact.

2,009 275
Explore
FreedomIntelligence/OpenClaw-Medical-Skills

bio-alignment-io

Read, write, and convert multiple sequence alignment files using Biopython Bio.AlignIO. Supports Clustal, PHYLIP, Stockholm, FASTA, Nexus, and other alignment formats for phylogenetics and conservation analysis. Use when reading, writing, or converting alignment file formats.

2,009 275
Explore
FreedomIntelligence/OpenClaw-Medical-Skills

sleep-analyzer

分析睡眠数据、识别睡眠模式、评估睡眠质量，并提供个性化睡眠改善建议。支持与其他健康数据的关联分析。

2,009 275
Explore
FreedomIntelligence/OpenClaw-Medical-Skills

metabolomics-workbench-database

Access NIH Metabolomics Workbench via REST API (4,200+ studies). Query metabolites, RefMet nomenclature, MS/NMR data, m/z searches, study metadata, for metabolomics and biomarker discovery.

2,009 275
Explore
FreedomIntelligence/OpenClaw-Medical-Skills

bio-hi-c-analysis-matrix-operations

Balance, normalize, and transform Hi-C contact matrices using cooler and cooltools. Apply iterative correction (ICE), compute expected values, and generate observed/expected matrices. Use when normalizing or transforming Hi-C matrices.

2,009 275
Explore

Didn't find tool you were looking for?

Be as detailed as possible for better results