bio-alignment-validation
Validate alignment quality with insert size distribution, proper pairing rates, GC bias, strand balance, and other post-alignment metrics. Use when verifying alignment data quality before variant calling or quantification.
npx skills add BioTender-max/awesome-bio-agent-skills --skill alignment-validation --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: matplotlib 3.8+, numpy 1.26+, picard 3.1+, pysam 0.22+, 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. # Alignment Validation Post-alignment quality control to verify alignment quality and identify issues. **"Check alignment quality"** → Compute post-alignment QC metrics (mapping rate, pairing, insert size, strand balance) to identify issues before downstream analysis. - CLI: `samtools flagstat`, `samtools stats`, Picard `CollectAlignmentSummaryMetrics` - Python: `pysam.AlignmentFile` iteration with metric calculations ## Two Different Validations | Concern | Tools | What it catches | |---------|-------|-----------------| | **File integrity** | `samtools quickcheck`, `picard ValidateSamFile` | Truncation, missing EOF, malformed records, wrong CIGAR, MAPQ out of range | | **Sequenc
- Version Compatibility
- Two Different Validations
- File Integrity
- Sequence Dictionary Cross-Validation (M5)
- Contamination and Sample Swap
- Insert Size Distribution
- samtools stats
- Picard CollectInsertSizeMetrics
- Expected Insert Sizes by Library
- Python Insert Size Analysis
- Proper Pairing Rate
- samtools flagstat
- Calculate Pairing Rate
- Expected Rates
samtools quickcheck -v in.bam || echo "QUICKCHECK FAILED" samtools quickcheck -v *.bam > bad_bams.fofn # one fail-line per bad file Slow but thorough: structural validation picard ValidateSamFile I=in.bam MODE=SUMMARY R=ref.fa picard ValidateSamFile I=in.bam MODE=SUMMARY R=ref.fa \ test -s in.bam \ Compare per-contig MD5 between BAM and reference diff \ Cross-sample contamination verifybamid2 --SVDPrefix /resources/1000g.b38.vcf.gz.SVD \
What does the bio-alignment-validation skill do?
Validate alignment quality with insert size distribution, proper pairing rates, GC bias, strand balance, and other post-alignment metrics. Use when verifying alignment data quality before variant calling or quantification.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill alignment-validation --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.