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Bioinformatics Fundamentals

Listed
delphine-l·vlatest·other

This skill provides foundational knowledge of bioinformatics concepts & techniques, aiding in understanding biological data analysis.

Repository

Install on your platform

Showing Claude Code. One command installs this skill into any of the agents below.

  1. 1

    Run this in your project

    terminal
    $ npx skills add delphine-l/claude_global --skill bioinformatics-fundamentals -a claude-code

  2. Uses the open-source skills CLI and needs Node.js. Add -g to install it for your user instead of this project.

What we know about this skill

Publisher

delphine-l

Taken from the source listing. We haven't verified who controls this account.

Install target

Live repository

Not pinned. Installing fetches whatever the repository holds at the time you run the command.

No human has reviewed this code. The checks below are a static scan of the files at one commit — nobody has run this skill or judged whether it works. A skill runs with whatever access you give your agent, so read the source before you install it.

Automated safety checks

scanned

This skill failed 1 of 6 checks. A failure is not proof of bad intent; it means something in the code needs a human to look at it before you run it.

  • No undeclared network calls: failed

    Contacts 1 host that is neither well-known infrastructure nor declared in the skill's frontmatter: ftp.ncbi.nlm.nih.gov.

    Every host the skill dials — from its scripts, its config endpoints or the commands it tells the agent to run — is either well-known package and API infrastructure or declared in its own frontmatter. Links in documentation are not counted.

    Hosts contacted

    ftp.ncbi.nlm.nih.govundeclared

    What it found

    • skills/bioinformatics/fundamentals/reference.md:813contacts ftp.ncbi.nlm.nih.gov
      wget https://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools/converters/by_program/agp_validate/linux64.agp_validate.gz

  • Declares what it does: passed

    SKILL.md parses and declares a name and a description.

    SKILL.md exists, its frontmatter parses, and it declares a name and a description.

  • No obfuscated payloads: passed

    No encoded or obfuscated payloads.

    No base64, hex or compressed blob is decoded and then executed, and no encoded shell commands.

  • No credential access: passed

    Reads no keys, tokens, keychains or credential files.

    Neither the code nor the SKILL.md instructions read SSH keys, cloud credentials, keychains, token stores, browser cookie databases or dotfiles that hold secrets.

  • No pipe-to-shell installers: passed

    No pipe-to-shell or download-and-run installers.

    No `curl … | sh` pattern, in the code or in the instructions, that runs code fetched at run time.

  • Pinned to a commit: passed

    Scanned delphine-l/claude_global at 71c292e8aa.

    The exact upstream commit SHA that was scanned is recorded, so the result refers to specific bytes.

Commit
71c292e8aa
Manifest
skills/bioinformatics/fundamentals/SKILL.md
Scanned
5 files, 2,783 lines
This is a static scan, not a review. It reads the skill's files; it does not run them, and it cannot tell you whether the skill is any good or whether the code does what its description says. A skill runs with whatever access you give your agent.
What each check looks for →

About this skill

What it does

This skill provides foundational knowledge about bioinformatics, genomics, and related workflows. It helps users understand common file formats like SAM/BAM and AGP, sequencing technologies such as PacBio HiFi and Illumina, and data processing patterns used in biological data analysis. The skill explains key concepts like mapping quality (MAPQ), CIGAR strings, and the meaning of SAM flags to aid in troubleshooting and interpretation of genomic data.

When to use it

  • Working with sequencing data from various technologies (PacBio HiFi, Hi-C, Illumina).
  • Debugging issues related to SAM/BAM alignment or filtering.
  • Processing AGP files for genome assembly curation.
  • Understanding paired-end versus single-end data.
  • Interpreting quality metrics like MAPQ and PHRED scores.
  • Troubleshooting empty outputs or broken read pairs in bioinformatics pipelines.

Key capabilities

  • Explanation of SAM/BAM file format, including flag combinations and their meanings.
  • Understanding of the "proper pair" flag and its implications for alignment.
  • Interpretation of Mapping Quality (MAPQ) scores and common thresholds.
  • Description of CIGAR strings and their representation of read alignments.
  • Overview of sequencing technologies like PacBio HiFi.

Example prompts

  • "Explain what a SAM flag with value 99 means."
  • "What is the significance of MAPQ scores in bioinformatics?"
  • "Describe how to interpret a CIGAR string like '50M5I45M'."

Tips & gotchas

  • This skill provides foundational knowledge; for complete details on SAM flags, CIGAR operations, and optional tags, refer to the referenced reference.md document.
  • The criteria for "proper pairs" can vary between different alignment tools, so be mindful of that when interpreting results.
  • A MAPQ score of 0 does not necessarily indicate an unmapped read; it could also signify equally good multiple mappings.