# Send Bioinformatics to your agent
Hand the extracted package to your coding agent with a concrete install brief instead of figuring it out manually.
## Fast path
- Download the package from Yavira.
- Extract it into a folder your agent can access.
- Paste one of the prompts below and point your agent at the extracted folder.
## Suggested prompts
### New install

```text
I downloaded a skill package from Yavira. Read SKILL.md from the extracted folder and install it by following the included instructions. Tell me what you changed and call out any manual steps you could not complete.
```
### Upgrade existing

```text
I downloaded an updated skill package from Yavira. Read SKILL.md from the extracted folder, compare it with my current installation, and upgrade it while preserving any custom configuration unless the package docs explicitly say otherwise. Summarize what changed and any follow-up checks I should run.
```
## Machine-readable fields
```json
{
  "schemaVersion": "1.0",
  "item": {
    "slug": "bioinformatics",
    "name": "Bioinformatics",
    "source": "tencent",
    "type": "skill",
    "category": "数据分析",
    "sourceUrl": "https://clawhub.ai/ivangdavila/bioinformatics",
    "canonicalUrl": "https://clawhub.ai/ivangdavila/bioinformatics",
    "targetPlatform": "OpenClaw"
  },
  "install": {
    "downloadUrl": "/downloads/bioinformatics",
    "sourceDownloadUrl": "https://wry-manatee-359.convex.site/api/v1/download?slug=bioinformatics",
    "sourcePlatform": "tencent",
    "targetPlatform": "OpenClaw",
    "packageFormat": "ZIP package",
    "primaryDoc": "SKILL.md",
    "includedAssets": [
      "SKILL.md",
      "formats.md",
      "memory-template.md",
      "rnaseq.md",
      "setup.md",
      "tools.md"
    ],
    "downloadMode": "redirect",
    "sourceHealth": {
      "source": "tencent",
      "slug": "bioinformatics",
      "status": "healthy",
      "reason": "direct_download_ok",
      "recommendedAction": "download",
      "checkedAt": "2026-04-29T01:45:43.266Z",
      "expiresAt": "2026-05-06T01:45:43.266Z",
      "httpStatus": 200,
      "finalUrl": "https://wry-manatee-359.convex.site/api/v1/download?slug=bioinformatics",
      "contentType": "application/zip",
      "probeMethod": "head",
      "details": {
        "probeUrl": "https://wry-manatee-359.convex.site/api/v1/download?slug=bioinformatics",
        "contentDisposition": "attachment; filename=\"bioinformatics-1.0.0.zip\"",
        "redirectLocation": null,
        "bodySnippet": null,
        "slug": "bioinformatics"
      },
      "scope": "item",
      "summary": "Item download looks usable.",
      "detail": "Yavira can redirect you to the upstream package for this item.",
      "primaryActionLabel": "Download for OpenClaw",
      "primaryActionHref": "/downloads/bioinformatics"
    },
    "validation": {
      "installChecklist": [
        "Use the Yavira download entry.",
        "Review SKILL.md after the package is downloaded.",
        "Confirm the extracted package contains the expected setup assets."
      ],
      "postInstallChecks": [
        "Confirm the extracted package includes the expected docs or setup files.",
        "Validate the skill or prompts are available in your target agent workspace.",
        "Capture any manual follow-up steps the agent could not complete."
      ]
    }
  },
  "links": {
    "detailUrl": "https://openagent3.xyz/skills/bioinformatics",
    "downloadUrl": "https://openagent3.xyz/downloads/bioinformatics",
    "agentUrl": "https://openagent3.xyz/skills/bioinformatics/agent",
    "manifestUrl": "https://openagent3.xyz/skills/bioinformatics/agent.json",
    "briefUrl": "https://openagent3.xyz/skills/bioinformatics/agent.md"
  }
}
```
## Documentation

### Setup

On first use, read setup.md for integration guidelines. Create ~/bioinformatics/ with user consent to store project context and preferences.

### When to Use

User needs to analyze biological sequences, run genomic pipelines, or interpret sequencing data. Agent handles sequence alignment, variant calling, expression analysis, and format conversions.

### Architecture

Memory lives in ~/bioinformatics/. See memory-template.md for structure.

~/bioinformatics/
├── memory.md         # Projects, preferences, reference genomes
├── pipelines/        # Saved pipeline configurations
└── results/          # Analysis outputs and logs

### Quick Reference

TopicFileSetup processsetup.mdMemory templatememory-template.mdFile formatsformats.mdTool commandstools.mdRNA-seq pipelinernaseq.mdVariant callingvariants.md

### 1. Verify Input Quality First

Before any analysis, check input data quality:

FASTQ: Run FastQC, check per-base quality, adapter content
BAM: Verify sorted, indexed (samtools quickcheck)
VCF: Validate format (bcftools view -h)

Bad input → garbage output. Always QC first.

### 2. Use Reference Genome Consistently

Track which reference is used per project:

Human: GRCh38/hg38 (prefer) or GRCh37/hg19
Mouse: GRCm39/mm39 or GRCm38/mm10
Mixing references = invalid results

Store reference info in ~/bioinformatics/memory.md per project.

### 3. Preserve Raw Data

NEVER modify original FASTQ/BAM files:

Work on copies
Keep originals read-only
Log every transformation step

### 4. Resource Awareness

Bioinformatics commands can consume massive resources:

Check file sizes before operations
Use streaming when possible (samtools view | ...)
Estimate memory needs (BWA: ~6GB for human genome)
Warn before operations >10 minutes

### 5. Reproducibility

Every analysis must be reproducible:

Log exact tool versions (samtools --version)
Save command parameters
Record input file checksums for critical analyses

### Common Traps

Wrong chromosome naming — chr1 vs 1 causes silent failures. Check and convert with sed 's/^chr//'
Unsorted BAM — Most tools expect sorted input. Symptoms: errors or wrong results with no warning
Index missing — BAM needs .bai, VCF needs .tbi. Commands fail cryptically without them
Memory exhaustion — Large BAM operations kill the session. Stream or use --threads wisely
Stale indices — After modifying BAM/VCF, regenerate index. Old index = corrupt reads
0-based vs 1-based coordinates — BED is 0-based, VCF/GFF is 1-based. Off-by-one bugs are common

### File Formats Quick Reference

FormatPurposeKey ToolFASTAReference sequencessamtools faidxFASTQRaw reads + qualityseqtk, fastpSAM/BAMAligned readssamtoolsVCF/BCFVariantsbcftoolsBEDGenomic intervalsbedtoolsGFF/GTFGene annotationsgffreadBigWigCoverage tracksdeepTools

### Quality Control

# FASTQ quality report
fastqc sample.fastq.gz -o qc_reports/

# Trim adapters + low quality
fastp -i R1.fq.gz -I R2.fq.gz -o R1.clean.fq.gz -O R2.clean.fq.gz

# BAM statistics
samtools flagstat aligned.bam
samtools stats aligned.bam > stats.txt

### Alignment

# Index reference (once)
bwa index reference.fa

# Align paired-end reads
bwa mem -t 8 reference.fa R1.fq.gz R2.fq.gz | \\
  samtools sort -o aligned.bam -

# Index BAM
samtools index aligned.bam

### Variant Calling

# Call variants
bcftools mpileup -Ou -f reference.fa aligned.bam | \\
  bcftools call -mv -Oz -o variants.vcf.gz

# Index VCF
bcftools index variants.vcf.gz

# Filter variants
bcftools filter -s LowQual -e 'QUAL<20' variants.vcf.gz

### Data Manipulation

# Extract region
samtools view -b aligned.bam chr1:1000000-2000000 > region.bam

# Convert BAM to FASTQ
samtools fastq -1 R1.fq.gz -2 R2.fq.gz aligned.bam

# Merge BAMs
samtools merge merged.bam sample1.bam sample2.bam

# Subset VCF by region
bcftools view -r chr1:1000-2000 variants.vcf.gz

### Security & Privacy

Data access:

Only reads files user explicitly provides as input
Writes outputs to directories user specifies
Stores preferences in ~/bioinformatics/ (with consent)

Data that stays local:

All sequence data processed locally
No external API calls for analysis
Pipeline configs in ~/bioinformatics/

This skill does NOT:

Upload sequence data anywhere
Access files without explicit user instruction
Infer or collect data beyond explicit inputs
Make network requests during analysis

Note: Installing tools (conda, brew) and downloading reference genomes requires internet access. These are user-initiated actions.

### Related Skills

Install with clawhub install <slug> if user confirms:

data-analysis — statistical interpretation
statistics — hypothesis testing
science — research methodology

### Feedback

If useful: clawhub star bioinformatics
Stay updated: clawhub sync
## Trust
- Source: tencent
- Verification: Indexed source record
- Publisher: ivangdavila
- Version: 1.0.0
## Source health
- Status: healthy
- Item download looks usable.
- Yavira can redirect you to the upstream package for this item.
- Health scope: item
- Reason: direct_download_ok
- Checked at: 2026-04-29T01:45:43.266Z
- Expires at: 2026-05-06T01:45:43.266Z
- Recommended action: Download for OpenClaw
## Links
- [Detail page](https://openagent3.xyz/skills/bioinformatics)
- [Send to Agent page](https://openagent3.xyz/skills/bioinformatics/agent)
- [JSON manifest](https://openagent3.xyz/skills/bioinformatics/agent.json)
- [Markdown brief](https://openagent3.xyz/skills/bioinformatics/agent.md)
- [Download page](https://openagent3.xyz/downloads/bioinformatics)