bio-alignment-validation skillA
bio-alignment-validation is agent-read markdown (skill) from pku-yuangroup/openai4s: 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..
Indexed from public GitHub and served as immutable, content-addressed versions. Install it pinned to an exact SHA-256 with the mdr CLI, and every file is verified against the hash recorded here before it reaches your agent. The deterministic audit below grades the latest version, and the same file always earns the same grade.
What the file says
## 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 | …
Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-alignment-validation@git:20260821.2d1b678mdr add pku-yuangroup/openai4s/bio-alignment-validation@sha256:6faae5baaa1ffdd8Pin to a label to follow the author's releases, or to a sha256 to freeze the exact bytes forever. Either way the resolved hash is written to mdr.lock, and mdr install reproduces it on any machine.
[](https://markdownregistry.com/a/art_mioygqmsoj62gmw4)
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Versions
Audit of the latest version
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- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (15095 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
pku-yuangroup/openai4s · 586 stars · license MIT · pushed 2026-09-23 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_mioygqmsoj62gmw4 GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-alignment-validation GET https://markdownregistry.com/api/v1/blob/6faae5baaa1ffdd86c51b6f7d3a7c2206dcba37fb6c49d195c58abbcf80cebfa
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