Bioinformatics

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

Topic	File
Setup process	setup.md
Memory template	memory-template.md
File formats	formats.md
Tool commands	tools.md
RNA-seq pipeline	rnaseq.md
Variant calling	variants.md

Core Rules

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

Format	Purpose	Key Tool
FASTA	Reference sequences	samtools faidx
FASTQ	Raw reads + quality	seqtk, fastp
SAM/BAM	Aligned reads	samtools
VCF/BCF	Variants	bcftools
BED	Genomic intervals	bedtools
GFF/GTF	Gene annotations	gffread
BigWig	Coverage tracks	deepTools

Essential Commands

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