Hermes — Bioinformatics Analysis Agent

Autonomous bioinformatics analysis platform running on a high-performance server (160 cores, 2.2 TiB RAM, Ubuntu 24.04).

Overview

Hermes provides a set of Snakemake workflows orchestrated via an MCP server, allowing Claude to plan, execute, and monitor bioinformatics analyses end-to-end.

Available Workflows

Workflow	Analysis Type	Key Tools
genome_annotation	Genome QC + Repeat + BRAKER4 + Functional	BUSCO, RepeatModeler, BRAKER4, DIAMOND, InterPro
rnaseq	RNA-seq differential expression	STAR, featureCounts, DESeq2, clusterProfiler
atacseq	ATAC-seq peak calling	Bowtie2, MACS3, DiffBind
scrnaseq	Single-cell RNA-seq clustering + markers	STARsolo, scDblFinder, Scanpy, Leiden
wgs_snp	WGS SNP/INDEL calling (non-model organisms)	fastp, BWA-MEM2, DeepVariant (GPU), GLnexus, SNPeff
snp_association	SNP-trait GWAS + Fst scan	PLINK2, GEMMA LMM, VCFtools Fst, CMplot
pool_seq	Pool-seq allele frequency + Fst scan	fastp, BWA-MEM2, bcftools, Hudson Fst (R)

Input Format

All workflows use standardized CSV samplesheets. See samplesheet_template.csv in each workflow directory.

Sequence workflows (wgs_snp, scrnaseq, rnaseq, atacseq)

sample,r1,r2
sample_001,/path/to/sample_001_R1.fastq.gz,/path/to/sample_001_R2.fastq.gz

GWAS metadata (snp_association)

sample_id,phenotype,weight_g,length_cm
fish_001,1,52.3,16.1
fish_031,0,41.7,14.5

Structure

hermes/
├── mcp_server.py          # MCP server (tools: run_workflow, get_status, etc.)
├── setup_hermes.sh        # Environment setup script
├── CLAUDE.md              # Agent instructions
└── workflows/
    ├── wgs_snp/
    ├── snp_association/
    ├── rnaseq/
    ├── scrnaseq/
    ├── atacseq/
    └── genome_annotation/

Key Paths (server-specific)

Databases     : /home/cylin/Vet_Hamaguri/databases/
FCS-GX DB     : /home/cylin/Vet_Hamaguri/FCS_DB
Workflow runs : /home/cylin/hermes/runs/<run_id>/

Requirements

• Snakemake ≥ 8
• Conda / Mamba
• Docker (for DeepVariant GPU)
• NVIDIA GPU + CUDA (for wgs_snp DeepVariant step)
• Claude Code with MCP server configured