Individual skill

tooluniverse-sequence-analysis

Biological sequence analysis — gene/protein sequence retrieval (NCBI, Ensembl, UniProt), nucleotide/protein search, ortholog discovery, and FASTQ QC + alignment workflows (Trimmomatic, BWA, samtools, coverage depth). Use for sequence retrieval, sequence comparison, FASTQ QC analysis, and read alignment pre-processing.

plugins/tooluniverse/skills/tooluniverse-sequence-analysis/SKILL.md

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Repository stars (not skill ratings): 1,778
Repository last updated: Nov 8, 2026
License: Apache-2.0

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SKILL.mdcore · 25,339 bytes
scripts/amino_acids.pyruns · 24,879 bytes
scripts/biology_facts.pyruns · 54,508 bytes
scripts/sequence_tools.pyruns · 13,318 bytes
scripts/translate_dna.pyruns · 2,291 bytes

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# Biological Sequence Analysis

## ⚠<U+FE0F> TOP-OF-MIND RULE: Trimmomatic "reads completely discarded" = `F + R + 2*D`, summed across samples

When a question asks about Trimmomatic "reads completely discarded" / "reads thrown out" /
"reads not in any output", do NOT report the `Dropped` field alone. `Dropped` counts
PAIRS where both mates failed; each pair = 2 individual reads. Plus the Forward-only and
Reverse-only buckets also discard one read per pair.

```
reads_discarded = sum over samples of (Forward_Only + Reverse_Only + 2 * Dropped)
```

❌ WRONG: `sum(Dropped per sample)` — typically reports ~thousands, GT is 100×+ higher