Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx agentmods add skills/gptomics/bioskills/alignment-sortingnpx skills add GPTomics/bioSkills --skill alignment-sortinggit clone --depth 1 https://github.com/GPTomics/bioSkillsWhat it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5 | $0.00037 | $0.02971 |
| Opus 5 | $0.00018 | $0.01486 |
| Sonnet 5 | $0.00007 | $0.00594 |
| Haiku 4.5 | $0.00004 | $0.00297 |
Grade A, and why
bio-alignment-sorting scanned grade A with 1 finding against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 2d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Runs shell commandslowCapability
Expected in a hook, worth knowing in a rule or an instructions file.
subprocess.run( Copies of this mod
1 near-identical copy found in the catalogue:
- bio-alignment-sorting — 97% identical, 12 lines differ
How it starts
The opening of the file, as written. The whole thing — 323 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: pysam 0.22+, samtools 1.19+
Before using code patterns, verify installed versions match. If versions differ:
- Python:
pip show <package>thenhelp(module.function)to check signatures - CLI:
<tool> --versionthen<tool> --helpto confirm flags
If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.
Alignment Sorting
Sort alignment files by coordinate or read name using samtools and pysam.
"Sort a BAM file" -> Reorder reads by genomic coordinate (for indexing/variant calling) or by name (for paired-end processing).
- CLI:
samtools sort -o sorted.bam input.bam - Python:
pysam.sort('-o', 'sorted.bam', 'input.bam')
Sort Orders
| Order | Flag | Use Case |
|---|---|---|
| Coordinate | default | Indexing, visualization, variant calling |
| Name | -n |
Paired-end processing, fixmate, markdup |
| Tag | -t TAG |
Sort by specific tag value |
samtools sort
Sort by Coordinate (Default)
samtools sort -o sorted.bam input.bam
Sort by Read Name
samtools sort -n -o namesorted.bam input.bam
Multi-threaded Sorting
samtools sort -@ 8 -o sorted.bam input.bam
Control Memory Usage
samtools sort -m 4G -@ 4 -o sorted.bam input.bam
Set Temporary Directory
samtools sort -T /tmp/sort_tmp -o sorted.bam input.bam
Specify Output Format
# Output as BAM (default)
samtools sort -O bam -o sorted.bam input.bam
# Output as CRAM
samtools sort -O cram --reference ref.fa -o sorted.cram input.bam
Sort by Tag
# Sort by cell barcode (10x Genomics)
samtools sort -t CB -o sorted_by_barcode.bam input.bam
Pipe from Aligner
bwa mem ref.fa reads.fq | samtools sort -o aligned.bam
samtools collate vs sort -n
| Tool | Algorithm | Speed | Memory | Output guarantee |
|---|---|---|---|---|
sort -n |
Full lexicographic sort by QNAME | Slowest | Spills to -T |
Strict total order by name |
collate |
Hash-bucket grouping | ~3-10x faster | Bounded | Mates adjacent; between-mate order undefined |
What ships with it
2 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 2d ago First seen · 323 lines · 37 tokens per session scan A f425e08b3819
bio-alignment-sorting is a skill published in the GitHub repository GPTomics/bioSkills (1,198 stars, last pushed 17d ago), licensed MIT. It adds 37 tokens to every session and 2,971 once invoked, about $0.0002 per session on Opus 5. A static security scan graded it A with 1 finding (runs shell commands). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.
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