Agent skill · research science · delphine-l
bioinformatics-fundamentals
Core bioinformatics concepts including SAM/BAM format, AGP genome assembly format, sequencing technologies (Hi-C, HiFi, Illumina), quality metrics, and common data processing patterns. Essential for debugging alignment, filtering, pairing issues, and AGP coordinate validation.
Why this skill is useful
Provides domain-specific knowledge on bioinformatics file formats and sequencing technologies that the AI wouldn't reliably generate on its own.
What it needs
About 8k tokens when loaded. Last updated 2026-05-14. 17 stars on the source repository.
What this skill does
Bioinformatics Fundamentals Foundation knowledge for genomics and bioinformatics workflows. Provides essential understanding of file formats, sequencing technologies, and common data processing patterns. When to Use This Skill Working with sequencing data (PacBio HiFi, Hi-C, Illumina) Debugging SAM/BAM alignment or filtering issues Processing AGP files for genome assembly curation Validating AGP coordinate systems and unloc assignments Understanding paired-end vs single-end data Interpreting quality metrics (MAPQ, PHRED scores) Troubleshooting empty outputs or broken read pairs Accessing GenomeArk QC data (GenomeScope, BUSCO, Merqury) Curating karyotype data or chromosome count analysis General bioinformatics data analysis SAM/BAM Format Essentials SAM Flags (Bitwise) Flags are additive - a read can have multiple flags set simultaneously. Common Flags: 0x0001 (1): Read is paired in sequencing 0x0002 (2): Each segment properly aligned (proper pair) 0x0004 (4): Read unmapped 0x0008 (8): Mate unmapped 0x0010 (16): Read mapped to reverse strand 0x0020 (32): Mate mapped to reverse strand 0x0040 (64): First in pair (R1/forward) 0x0080 (128): Second in pair (R2/reverse) 0x0100 (256): Secondary alignment 0x0400 (1024): PCR or optical duplicate 0x0800 (2048): Supplementary alignment Flag Combinations: Properly paired R1: 99 (0x63 = 1 + 2 + 32 + 64) Properly paired R2: 147 (0x93 = 1 + 2 + 16 + 128) Unmapped read: 4 Mate unmapped: 8 See reference.md for complete flag tables, CIGAR operations, optional tags, and SAM mandatory fields. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills delphine-l/fundamentals