bio-rna-quantification-alignment-free-quant SKILL.md skillA
bio-rna-quantification-alignment-free-quant from fridrichmethod/awesome-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add fridrichmethod/awesome-skills/bio-rna-quantification-alignment-free-quant@git:20260628.aa12f9bPins git:20260628.aa12f9b in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- fridrichmethod/awesome-skills
- Path
skills/alignment-free-quant/SKILL.md- Versions recorded
- 3
- Latest version
- git:20260628.aa12f9b, committed Jun 28, 2026
- First version recorded
- May 17, 2026
- Size
- 10,880 bytes
- Repository stars
- 15
- License
- a license file GitHub does not identify
Quantify transcript expression from FASTQ with Salmon (selective alignment) or kallisto (pseudoalignment), bypassing genome mapping. Use when quantifying RNA-seq without alignment, deciding whether a decoy-aware index is required, detecting and verifying library strandedness, enabling GC and sequence bias correction, or choosing whether to generate inferential replicates (bootstraps/Gibbs) for transcript-level downstream testing.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
## Version Compatibility Reference examples tested with: Salmon 1.10+, kallisto 0.50+, fastp 0.23+, pandas 2.2+ Before using code patterns, verify installed versions match. If versions differ: - 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-Free Quantification **"Quantify gene expression without aligning to the genome"** -> Estimate transcript abundances directly from FASTQ reads by mapping to a transcriptome, then resolving multi-mapping reads (paralogs, shared isoform sequence) with an EM/variational model. - CLI: `salmon quant -i index -l A -1 R1.fq.gz -2 R2.fq.gz -o quant/`, `kallisto quant -i index -o out R1.fq.gz R2.fq.gz` …
Read the whole file at its exact version.
How to install
mdr add fridrichmethod/awesome-skills/bio-rna-quantification-alignment-free-quant@sha256:d8a61bb9dc404447The line at the top of this page pins the label git:20260628.aa12f9b, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_ogpjvropm72bi7ka)
1 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 3 versions of this file, between May 17, 2026 and Jun 28, 2026, about one every 21 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260628.aa12f9b latest | 2026-06-28 | aa12f9b | 10,880 B | A | view · diff |
| git:20260531.6e617c4 | 2026-05-31 | 6e617c4 | 6,028 B | A | view · diff |
| git:20260517.81511a7 | 2026-05-17 | 81511a7 | 6,029 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (10880 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
fridrichmethod/awesome-skills · 15 stars · license a license file GitHub does not identify · pushed 2026-10-18 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_ogpjvropm72bi7ka GET https://markdownregistry.com/api/v1/resolve?ref=fridrichmethod/awesome-skills/bio-rna-quantification-alignment-free-quant GET https://markdownregistry.com/api/v1/blob/d8a61bb9dc40444749773ef9045cd673effcca48e1b90b8089bf6d381aa1b810
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.