bio-genome-intervals-coverage-analysis
Calculate read depth and coverage across genomic intervals using bedtools genomecov and coverage. Generate bedGraph files, compute per-base depth, and summarize coverage statistics. Use when assessing sequencing depth, creating coverage tracks, or evaluating target capture efficiency.
npx skills add BioTender-max/awesome-bio-agent-skills --skill coverage-analysis --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.
## 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>` then `help(module.function)` to check signatures - CLI: `<tool> --version` then `<tool> --help` to 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) ```bash # 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
- Version Compatibility
- genomecov - Genome-wide Coverage
- Per-base Coverage (bedGraph)
- Coverage Histogram
- Coverage from BED
- Python
- coverage - Coverage per Feature
- Basic Coverage
- Coverage Options
- multicov - Counts Across Multiple BAMs
- Calculate Coverage Statistics
- Mean/Median Depth
- Coverage Distribution
- Common Patterns
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) bedtools genomecov -ibam alignments.bam -bg -scale $SCALE > normalized.bedGraph Use only 5' end of reads
What does the bio-genome-intervals-coverage-analysis skill do?
Calculate read depth and coverage across genomic intervals using bedtools genomecov and coverage. Generate bedGraph files, compute per-base depth, and summarize coverage statistics. Use when assessing sequencing depth, creating coverage tracks, or evaluating target capture efficiency.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill coverage-analysis --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.