# Bioinformatics Toolkit

> Use when you need a workspace-level entry point to choose among the installed bioinformatics CLIs and repo-backed AI/bio projects in this environment.

- Skill: `vimalinx/bioinformatics-toolkit` (Agent Skill, multi-file: 5 files)
- Install (CLI): `npx skillmds add vimalinx/bioinformatics-toolkit`
- Raw SKILL.md: https://api.skillmd.com/api/skills/vimalinx/bioinformatics-toolkit/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- Author: vimalinx (https://skillmd.com/u/vimalinx)
- Updated: 2026-09-09
- Page: https://skillmd.com/skills/vimalinx/bioinformatics-toolkit

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# bioinformatics-toolkit

Top-level workspace gateway for bioinformatics work. In this environment, the most reliable local assets are the `bio` conda env CLIs (`blast*`, `bowtie2`, `bwa`, `samtools`, `bcftools`, `prodigal`, `RNAfold`, `iqtree`, `hmmscan`, `mafft`, `muscle`, `hisat2`, `featureCounts`, `seqkit`) plus several repo-backed projects under `repositories/active/` such as `Biomni`, `evo2`, and `RFdiffusion`.

## Quick Start

- **Activate environment:** `conda activate bio`
- **Verified local CLI families:** BLAST, Bowtie2, BWA, Samtools, Bcftools, HMMER, MAFFT, MUSCLE, Prodigal, ViennaRNA, IQ-TREE, SeqKit
- **Repo-backed projects:** `/home/vimalinx/Projects/bio_studio/repositories/active/Biomni`, `/home/vimalinx/Projects/bio_studio/repositories/active/evo2`, `/home/vimalinx/Projects/bio_studio/repositories/active/RFdiffusion`

## When To Use This Tool

- Figuring out which local tool family or project should handle a bioinformatics request
- Starting from a workspace-wide inventory instead of guessing what is installed
- Routing between plain CLIs, teaching projects, and heavier repo-backed AI workflows
- Auditing whether a proposed method matches the actual assets in this workspace

## Common Patterns

```bash
# Check the core local CLI toolchain
command -v blastn bowtie2 bwa samtools bcftools prodigal RNAfold iqtree
```

```bash
# Start a classic alignment + BAM-processing workflow
bowtie2 -x ref_index -U reads.fq -S aligned.sam
samtools view -bS aligned.sam | samtools sort -o aligned.sorted.bam
```

```bash
# Start an RNA structure or phylogeny workflow
RNAfold < sequences.fa
iqtree -s alignment.fa
```

```bash
# Inspect repo-backed bio projects
ls /home/vimalinx/Projects/bio_studio/repositories/active
```

## Recommended Workflow

1. Begin with the verified CLI inventory in the `bio` environment.
2. Route the task to a narrower skill whenever the job has a clear domain: sequence analysis, protein structure/design, yeast learning project, Biomni, Evo 2, or RFdiffusion.
3. Use repo-backed projects only after confirming their extra dependencies are satisfied.
4. Keep the umbrella skill focused on tool selection and environment reality checks, not on pretending every downstream project is already turnkey.

## Guardrails

- The reliable base layer here is the installed CLI toolchain in the `bio` environment.
- Repo-backed projects like Biomni, Evo 2, and RFdiffusion are present locally but each has additional setup gaps or missing dependencies.
- Do not advertise absent tools just because earlier autogenerated docs mentioned them. Limit recommendations to commands or repos that are actually present.
- When in doubt, prefer the narrower skill that matches the concrete subtask.