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 skills add thesecondfox/skill --skill bio-genome-intervals-coverage-analysisgit clone --depth 1 https://github.com/thesecondfox/skillWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/thesecondfox/skill/bio-genome-intervals-coverage-analysis)<a href="https://agentmods.dev/skills/thesecondfox/skill/bio-genome-intervals-coverage-analysis"><img src="https://agentmods.dev/badge/skills/thesecondfox/skill/bio-genome-intervals-coverage-analysis/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/thesecondfox/skill/bio-genome-intervals-coverage-analysis"><img src="https://agentmods.dev/badge/skills/thesecondfox/skill/bio-genome-intervals-coverage-analysis.svg" alt="Reviewed on agentmods" width="80" height="20"></a>What 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 5.1 | $0.00057 | $0.02295 |
| Opus 5.5 | $0.00023 | $0.00918 |
| Sonnet 5.5 | $0.00011 | $0.00459 |
| Haiku 4.5 | $0.00006 | $0.00230 |
Grade A, and why
bio-genome-intervals-coverage-analysis 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 1mo 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.
result = subprocess.run(['samtools', 'view', '-c', 'alignments.bam'], How it starts
The opening of the file, as written. The whole thing — 300 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: bedtools 2.31+, numpy 1.26+, pandas 2.2+, 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.
Coverage Analysis
"Calculate sequencing coverage" → Compute per-base or per-region depth from BAM files to assess sequencing adequacy.
- CLI:
bedtools genomecov -ibam input.bam,samtools depth input.bam - Python:
pybedtools.BedTool('input.bam').genome_coverage()(pybedtools)
Calculate coverage and depth across genomic regions using bedtools and pybedtools.
genomecov - Genome-wide Coverage
Per-base Coverage (bedGraph)
# Generate bedGraph from BAM (per-base depth)
bedtools genomecov -ibam alignments.bam -bg > coverage.bedGraph
# Include zero-coverage regions
bedtools genomecov -ibam alignments.bam -bga > coverage_with_zeros.bedGraph
# Split by strand
bedtools genomecov -ibam alignments.bam -bg -strand + > plus_strand.bedGraph
bedtools genomecov -ibam alignments.bam -bg -strand - > minus_strand.bedGraph
# Scale by total reads (RPM normalization)
TOTAL=$(samtools view -c alignments.bam)
SCALE=$(echo "scale=10; 1000000/$TOTAL" | bc)
bedtools genomecov -ibam alignments.bam -bg -scale $SCALE > normalized.bedGraph
# Use only 5' end of reads
bedtools genomecov -ibam alignments.bam -bg -5 > five_prime.bedGraph
# Use only 3' end of reads
bedtools genomecov -ibam alignments.bam -bg -3 > three_prime.bedGraph
Coverage Histogram
# Genome-wide coverage histogram
bedtools genomecov -ibam alignments.bam > coverage_hist.txt
# Output format: chr, depth, bases_at_depth, chr_size, fraction
# genome 0 1000000 10000000 0.1
# genome 1 5000000 10000000 0.5
# ...
What ships with it
1 file 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.
- 1mo ago First seen · 300 lines · 57 tokens per session scan A f27b81fc074e
bio-genome-intervals-coverage-analysis is a skill published in the GitHub repository thesecondfox/skill (3 stars, last pushed 6mo ago), licensed MIT. It adds 57 tokens to every session and 2,295 once invoked, about $0.0002 per session on Opus 5.5. 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 2026-09-03.
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