albert-ying/.autolab/acquired_skills/spades-assembly
.autolab/acquired_skills/spades-assembly/SKILL.md
# 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
$ install --global
skillsauthnpx skillsauth add albert-ying/autonomous-lab .autolab/acquired_skills/spades-assemblyInstall 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 PM4.3s1 file scanned
SKILL.md
SPAdes Assembly Skill
When to Use
Use for de novo genome assembly when no reference genome is available.
Standard Workflow
- Run SPAdes:
spades.py -1 R1.fastq.gz -2 R2.fastq.gz -o assembly_output --careful - Check assembly stats: look at scaffolds.fasta or contigs.fasta
- Use assembled genome as reference for read mapping
Key Decisions
- Use
--carefulflag for bacterial genomes to reduce misassemblies - For small bacterial genomes, default k-mer sizes work well
- Output scaffolds.fasta is typically preferred over contigs.fasta
- Assembly quality can be checked with QUAST
- For experimental evolution: assemble ancestor, use as reference for evolved lines
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/snpeff
development
VerifiedTrustedCommunity
# SnpEff Skill ## When to Use Use for annotating variants with gene names, functional effects, and impact predictions. ## Standard Workflow 1. Build custom database from GFF/GBK + genome: - Create snpEff config entry - Place genome and genes files in data directory - Run: `snpEff build -gff3 custom_db` 2. Annotate VCF: `snpEff ann custom_db variants.vcf > annotated.vcf` 3. Parse annotations from ANN field in VCF ## Key Decisions - For custom/assembled genomes: build a local SnpEff da
7SKILL.mdUpdated Apr 3, 2026