bioinformatics-fundamentals — Claude Code skill: formats and QC
A skill that gives your agent the basics of SAM/BAM, AGP and sequencing. Useful when region filters return an empty BAM or break read pairs.
npx skills add Delphine-L/claude_global --skill bioinformatics-fundamentals -a claude-code
npx skills add Delphine-L/claude_global --skill fundamentals -a claude-codeWhat bioinformatics-fundamentals does
The skill hands your agent reference knowledge for genomics: SAM bitwise flags, CIGAR, MAPQ, the AGP assembly format, and how PacBio HiFi, Hi-C and Illumina data behave. Inside are flag tables, breakdowns of common mistakes, and command patterns for samtools and bamtools. The agent pulls this in when you debug alignment, filtering or assembly coordinates.
The usual trap is filtering paired reads by region. Apply -L with a BED file first and then a pair filter, and the pairs fall apart — you get an empty file. The correct order is the reverse: -f 2 first, region second. The skill explains why, and notes that isProperPair in bamtools is stricter than samtools -f 2.
It needs Read, Grep, Glob and Bash, since it reads files and runs commands like samtools view. One thing to keep in mind: Hi-C pairs are meant to land on distant loci, so region filtering breaks them more easily than anything else. Check pair counts before and after, don't trust the number at a glance.
What it helps with
- decode SAM bitwise flags and build the right combination
- fix an empty BAM after region filtering
- validate AGP coordinates and unloc assignments
- tell a proper pair from a flag match
- pick a mapper for HiFi, Hi-C or short reads
Example prompts for the agent
- Why does samtools view with -L regions.bed give me an empty BAM on paired reads?
- Break down flags 99 and 147 — is that a proper pair?
- Check this AGP assembly file for coordinate and unloc errors
How to install bioinformatics-fundamentals
1Skills CLI (Vercel)
npx skills add Delphine-L/claude_global --skill bioinformatics-fundamentals -a claude-codenpx skills add Delphine-L/claude_global --skill fundamentals -a claude-code2Manually: put the files in place
~/.claude/skills/fundamentals/SKILL.mdCopy the whole skill folder; for one project use .claude/skills/fundamentals/
1Skills CLI (Vercel)
npx skills add Delphine-L/claude_global --skill fundamentals -a codex2Manually: put the files in place
.agents/skills/fundamentals/SKILL.mdFor all projects use ~/.agents/skills/
1Skills CLI (Vercel)
npx skills add Delphine-L/claude_global --skill fundamentals -a cursor2Manually: put the files in place
.cursor/skills/fundamentals/SKILL.mdCursor also reads .agents/skills/ and .claude/skills/
1GitHub CLI
gh skill install Delphine-L/claude_global fundamentals2Manually: put the files in place
.github/skills/fundamentals/SKILL.md1Skills CLI (Vercel)
npx skills add Delphine-L/claude_global --skill fundamentals -a gemini-cli2Platform CLI
gemini skills install https://github.com/Delphine-L/claude_global --path skills/bioinformatics/fundamentalsManually: put the files in place
.devin/skills/fundamentals/SKILL.mdThe legacy .windsurf/skills/ path still works
Skills CLI (Vercel)
npx skills add Delphine-L/claude_global --skill fundamentals -a opencodeClaude.ai
Zip the folder and upload it in Settings → Capabilities → Skills
Step by step, with commands for each platform: How to install skills in Claude Code: five ways
Questions about bioinformatics-fundamentals
How do I install bioinformatics-fundamentals in Claude?
Run npx skills add Delphine-L/claude_global --skill bioinformatics-fundamentals -a claude-code. The skill lands in ~/.claude/skills/fundamentals/SKILL.md.
What does bioinformatics-fundamentals do?
It gives the agent core genomics concepts: SAM/BAM flags, CIGAR, MAPQ, the AGP format and sequencing traits. That helps it debug alignment and filtering problems.
How is bamtools filter different from samtools view -f 2?
isProperPair in bamtools is stricter — it checks pair validity more thoroughly than the -f 2 flag filter in samtools.
