albert-ying/autonomous-lab/spades-assembly
Claude Code and agent skill by albert-ying/autonomous-lab
Trust tier 3
- community
Source check pending
Checking that the SKILL.md file is still in the repository.
Install
npx vskill@latest install albert-ying/autonomous-lab/spades-assemblySKILL.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
Security
- Security scanPassed, 90 of 100Pattern checks on the skill's files.
- Model reviewPassed
Quality evaluation
- Task evaluationNot runNo evaluation yet. Run one in Skill Studio.
Source
- SKILL.md in the repositoryChecking.autolab/acquired_skills/spades-assembly/SKILL.md
Popularity
- 7-day trend score
- 5
Not refreshed yet.
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