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.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-longread-alignment --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.
## 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 | \ sam
- Version Compatibility
- Oxford Nanopore Alignment
- PacBio HiFi Alignment
- PacBio CLR Alignment
- Pre-Build Index for Multiple Runs
- Common Options
- Splice-Aware Alignment (RNA)
- With Junction BED (Known Splice Sites)
- Assembly to Reference Alignment
- Output PAF (Faster, No BAM)
- Keep Secondary and Supplementary
- Filter Alignments
- Multiple FASTQ Files
- Output Statistics
Basic ONT alignment minimap2 -ax map-ont reference.fa reads.fastq.gz | \ samtools sort -o aligned.bam samtools index aligned.bam PacBio HiFi reads (high accuracy) minimap2 -ax map-hifi reference.fa reads.fastq.gz | \ PacBio CLR (continuous long reads, lower accuracy) minimap2 -ax map-pb reference.fa reads.fastq.gz | \ Build index once minimap2 -d reference.mmi reference.fa
What does the bio-longread-alignment skill do?
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.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-longread-alignment --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 FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 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.