bio-tools
Biology research tools reference. Always available inside agent containers.
npx skills add BioTender-max/awesome-bio-agent-skills --skill bio-tools --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Bio Tools Reference You are running inside a BioClaw container with the following biology tools pre-installed. **Layout:** Runnable plot/PyMOL scripts live under `templates/` (synced to `/home/node/.claude/skills/bio-tools/templates/`). ## Quick Reference ### Sequence Search ```bash # Nucleotide BLAST blastn -query input.fa -subject ref.fa -outfmt 6 -evalue 1e-5 # Protein BLAST blastp -query protein.fa -subject ref_protein.fa -outfmt 6 # Translate then search blastx -query nucleotide.fa -subject protein_db.fa -outfmt 6 ``` ### Read Alignment ```bash # Index reference bwa index reference.fa # Align short reads bwa mem reference.fa reads_R1.fq reads_R2.fq > aligned.sam # Long reads minimap2 -a reference.fa long_reads.fq > aligned.sam # SAM to sorted BAM samtools view -bS aligned.sam | samtools sort -o sorted.bam samtools index sorted.bam ``` ### Quality Control ```bash # FastQC report fastqc reads.fq -o qc_output/ # FASTA/FASTQ stats seqtk comp reads.fq | head seqtk size reads.fq ``` ### Genome Arithmetic ```bash # Intersect two BED files bedtools intersect -a regions.bed -b features.bed # Coverage bedtools coverage -a regions.bed -b aligned.bam # Get FASTA from BED regions bedtool
- Quick Reference
- Sequence Search
- Read Alignment
- Quality Control
- Genome Arithmetic
- Python Quick Recipes
- Important Notes
- Reusable Figure Templates
- Volcano Plot Template
- QC Summary Plot Template
- PyMOL Render Template
- Inline Plot Snippets (Heatmap, PCA, Bar)
- Publication-Ready Plots (cnsplots)
- Genome Browser Tracks (pyGenomeTracks)
Nucleotide BLAST blastn -query input.fa -subject ref.fa -outfmt 6 -evalue 1e-5 Protein BLAST blastp -query protein.fa -subject ref_protein.fa -outfmt 6 Translate then search blastx -query nucleotide.fa -subject protein_db.fa -outfmt 6 Index reference bwa index reference.fa Align short reads bwa mem reference.fa reads_R1.fq reads_R2.fq > aligned.sam
What does the bio-tools skill do?
Biology research tools reference. Always available inside agent containers.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill bio-tools --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.