albert-ying/.autolab/acquired_skills/kraken2
.autolab/acquired_skills/kraken2/SKILL.md
# Kraken2 - Taxonomic Classification ## When to Use Use Kraken2 for taxonomic classification of metagenomic sequencing reads against a reference database. ## Standard Workflow 1. Install: `conda install -c bioconda kraken2` or `brew install kraken2` 2. Run classification: `kraken2 --db <db_path> --paired <R1.fastq.gz> <R2.fastq.gz> --output <output.txt> --report <report.txt> --threads <N>` 3. Key output files: - output.txt: per-read classification - report.txt: summary report with read c
$ install --global
skillsauthnpx skillsauth add albert-ying/autonomous-lab .autolab/acquired_skills/kraken2Install this skill globally with one command. Works with Claude Code, Cursor, and Windsurf.
Security Scan Results
3 of 9 scanners reported clean
Some scanners were skipped, did not run, or reported a non-clean status. Review each row below.
3
Scanners Passed
9
Scanners in report
Clean
TrivyContainer and dependency vulnerability scanner
95%
Clean
SemgrepStatic code analysis for vulnerabilities
95%
Clean
mcp-scan (Snyk)Model Context Protocol security validation
95%
Skipped
Snyk (dep)Open source security scanning
50%
Skipped
Socket.devSupply chain security analysis
50%
Skipped
VirusTotalMulti-engine malware detection
50%
Skipped
CrowdStrikeAdvanced threat intelligence
50%
Skipped
OSV-ScannerOpen Source Vulnerability database check
50%
Skipped
OWASP Dep-Check
50%
Last scanned: Apr 3, 2026, 9:39 PM3.9s1 file scanned
SKILL.md
Kraken2 - Taxonomic Classification
When to Use
Use Kraken2 for taxonomic classification of metagenomic sequencing reads against a reference database.
Standard Workflow
- Install:
conda install -c bioconda kraken2orbrew install kraken2 - Run classification:
kraken2 --db <db_path> --paired <R1.fastq.gz> <R2.fastq.gz> --output <output.txt> --report <report.txt> --threads <N> - Key output files:
- output.txt: per-read classification
- report.txt: summary report with read counts per taxon
Key Parameters
--db: path to Kraken2 database (directory containing hash.k2d, opts.k2d, taxo.k2d)--paired: for paired-end reads--report: generate summary report--confidence: confidence threshold (0-1, default 0)--threads: number of threads
Key Decisions
- Confidence threshold affects sensitivity vs specificity tradeoff
- Database choice determines which taxa can be identified
Related Skills
albert-ying/scientific-analysis-review
development
VerifiedTrustedCommunity
Critically review AI-agent-conducted scientific analyses for correctness, rigor, and completeness. Use this skill whenever an analysis session has completed and needs validation, when a user asks to "review," "validate," "check," or "audit" a computational analysis, or when an agent pipeline produces scientific results that require quality control before reporting. Also trigger when the user references an execution trace, notebook, or conversation history from a prior analysis session. This skill should run as the final step of any autonomous scientific analysis pipeline.
7SKILL.mdUpdated Apr 3, 2026
albert-ying/.autolab/acquired_skills/variant-calling
tools
VerifiedTrustedCommunity
# Variant Calling Skill ## When to Use Use when calling SNPs and indels from aligned BAM files against a reference. ## Standard Workflow 1. Mark duplicates (optional): `samtools markdup` 2. Call variants with freebayes: `freebayes -f reference.fasta -p 1 sample.bam > variants.vcf` OR with bcftools: `bcftools mpileup -f ref.fa sample.bam | bcftools call -mv -Oz -o variants.vcf.gz` 3. Filter variants: `bcftools filter -s LowQual -e 'QUAL<20' variants.vcf` ## Key Decisions - For haploid organ
7SKILL.mdUpdated Apr 3, 2026
albert-ying/.autolab/acquired_skills/trimmomatic
tools
VerifiedTrustedCommunity
# Trimmomatic - Read Quality Trimming ## When to Use Use Trimmomatic to trim adapter sequences and low-quality bases from Illumina sequencing reads. ## Standard Workflow 1. Install: `conda install -c bioconda trimmomatic` 2. Run: `trimmomatic PE <input_R1.fastq.gz> <input_R2.fastq.gz> <output_R1_paired.fastq.gz> <output_R1_unpaired.fastq.gz> <output_R2_paired.fastq.gz> <output_R2_unpaired.fastq.gz> ILLUMINACLIP:<adapters.fa>:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36` ## Key Pa
7SKILL.mdUpdated Apr 3, 2026
albert-ying/.autolab/acquired_skills/spades-assembly
testing
VerifiedTrustedCommunity
# SPAdes Assembly Skill ## When to Use Use for de novo genome assembly when no reference genome is available. ## Standard Workflow 1. Run SPAdes: `spades.py -1 R1.fastq.gz -2 R2.fastq.gz -o assembly_output --careful` 2. Check assembly stats: look at scaffolds.fasta or contigs.fasta 3. Use assembled genome as reference for read mapping ## Key Decisions - Use `--careful` flag for bacterial genomes to reduce misassemblies - For small bacterial genomes, default k-mer sizes work well - Output scaf
7SKILL.mdUpdated Apr 3, 2026