Extended-BioAgentBench

A growing benchmark for evaluating LLM agents on complex bioinformatics workflows.

Building on BioAgentBench (10 tasks), this benchmark adds 71 new tasks that test LLM agents on increasingly complex, multi-tool bioinformatics pipelines. Tasks span 6 domains and range from simple linear workflows to depth-8 diamond DAGs with 16+ CLI tools.

This benchmark is actively growing — new tasks are added continuously to cover more domains, increase complexity, and push the boundaries of what AI agents can do in bioinformatics.

What makes this benchmark different?

• Diamond DAG complexity: Tasks require running multiple independent tool branches that converge — not just linear pipelines
• No pipeline leakage: Task prompts describe what to produce, never which tools to use or how to structure the pipeline
• Domain-specific traps: Tasks include steps where default parameters silently produce wrong results (e.g., Tn5 shift correction in ATAC-seq, Medaka model selection for Nanopore)
• Real public data: Every task uses published datasets with ground truth generated by validated reference pipelines

Tasks (71 total)

#	Task ID	Name
11	chipseq-peak-calling	ChIP-seq Peak Calling: TAL1 Binding Site Comparison
12	bacterial-assembly	Bacterial Genome Assembly and Annotation: MRSA Characte
13	mobile-elements	Bacterial Mobile Genetic Element Characterization: MRSA
14	outbreak-investigation	Foodborne Pathogen Outbreak Investigation via WGS Phylo
15	atacseq-accessibility	ATAC-seq Chromatin Accessibility Profiling
16	longread-assembly	Nanopore Long-read Bacterial Genome Assembly
17	hybrid-assembly	Hybrid Genome Assembly from Illumina and Nanopore Data
18	sv-detection	Bacterial Structural Variant and SNP Detection
19	pangenome-evolution	E. coli Pan-genome and Core Phylogeny
20	metagenomic-profiling	Metagenomic Assembly and Functional Profiling
21	phage-characterization	Bacteriophage Genome Assembly and Functional Characteri
22	genome-comparison	Pairwise Bacterial Genome Comparison
23	mapping-qc	Genome Mapping and Coverage Quality Assessment
24	multisample-variants	Multi-sample Variant Calling and Comparison
25	consensus-genome	Bacterial Consensus Genome Generation
26	gene-prediction	Gene Prediction Method Comparison
27	downsampling-analysis	Read Downsampling and Assembly Quality Titration
28	plasmid-typing	Plasmid Detection and Replicon Typing
29	genome-completeness	Genome Completeness and Quality Assessment
30	species-identification	Multi-reference Bacterial Species Identification
31	viral-amplicon	Viral Amplicon Surveillance Analysis
32	bisulfite-methylation	Bisulfite Sequencing DNA Methylation Analysis
33	rnaseq-isoform	RNA-seq Isoform Assembly and Quantification
34	ancient-dna	Ancient DNA Authentication and Damage Assessment
35	mirna-seq	Small RNA-seq miRNA Discovery and Quantification
36	gcms-metabolomics	GC-MS Metabolomics Profiling: Brown Algae Salinity Adap
37	cutandrun	CUT&RUN Epigenomic Profiling
38	scrna-full-pipeline	Single-Cell RNA-seq Full Pipeline: Multi-Quantifier Ana
39	crispr-screen	CRISPR Screen Analysis: Drug Sensitivity Gene Discovery
40	amplicon-microbiome	16S Amplicon Microbiome: Community Profiling and Functi
41	rna-fusion	RNA Fusion Detection from RNA-seq
42	spatial-transcriptomics	Spatial Transcriptomics: Visium FFPE Brain Cancer Analy
43	taxonomic-profiling	Multi-classifier Taxonomic Profiling of Metagenomic Rea
44	lcms-metabolomics	LC-MS Untargeted Metabolomics: Urine Feature Discovery
45	somatic-variant-calling	Somatic Variant Calling: Tumor-Normal Paired Analysis
46	amr-bgc-screening	Antimicrobial Resistance and Biosynthetic Gene Cluster
47	variant-trio	Variant Annotation Trio: Clinical Interpretation of Ash
48	clinical-metaproteomics	Clinical Metaproteomics: Multi-Engine Marine Microbiome
49	mhc-immunopeptidomics	MHC Immunopeptidomics: Peptide Identification and Quant
50	riboseq	Ribosome Profiling Translation Analysis
51	neoantigen-prediction	Neoantigen Prediction: Tumor-Normal Somatic Analysis
52	somatic-germline-dual	Somatic+Germline Dual Analysis: Hereditary Cancer Varia
53	hicar-chromatin	HiCAR Chromatin Interaction: Proximity Ligation and Acc
54	radseq-popgen	RADseq Population Genetics: Stickleback Freshwater-Mari
55	mag-recovery	MAG Recovery: Metagenome-Assembled Genomes from Environ
56	viral-phylodynamics	Viral Phylodynamics (Molecular Clock Analysis)
57	edna-metabarcoding	eDNA Aquatic Metabarcoding Biodiversity Assessment
58	metatranscriptomics	Metatranscriptomics: Active Microbial Community Profili
59	nascent-transcription	Nascent Transcription: GRO-seq Polymerase Activity Prof
60	circrna-discovery	Circular RNA Discovery: C. elegans Wild-type vs fust-1
61	hic-3d-conformation	Hi-C 3D Genome Conformation Analysis
62	genome-scaffolding	Long-Read Genome Scaffolding of Fragmented Assembly
63	longread-rna-isoform	Long-Read RNA Isoform Discovery from Direct RNA Sequenc
64	circrna-detection	Circular RNA Detection and Quantification
65	pharmacogenomics	CYP2D6 Pharmacogenomic Star Allele Calling
66	rna-editing-detection	RNA Editing Detection: A-to-I Editing from Matched RNA/
67	cnv-detection-wes	CNV Detection from Whole-Exome Sequencing
68	haplotype-phasing	Haplotype Phasing and Genotype Refinement
69	dda-proteomics-simple	DDA Proteomics: Single-Engine BSA Identification
70	immune-repertoire	Immune Repertoire Analysis (BCR-seq)
71	germline-wes-gatk	Germline WES Variant Calling: Clinical Exome Analysis
72	gwas-association	GWAS Population Association Testing
73	dia-proteomics	Label-Free Proteomics: BSA Standard Identification
74	structural-variant-multi	Structural Variant Detection: Multi-caller Human SV Ana
75	dda-lfq-proteomics	DDA Label-Free Quantitative Proteomics
76	clinical-wgs-interpretation	Clinical WGS Interpretation: Full Clinical Genome Analy
77	repeat-element-annotation	Repeat Element Annotation (Transposable Element Analysi
78	msi-detection	Microsatellite Instability Detection: Multi-Caller Cons
79	scatac-seq	Single-Cell ATAC-seq Chromatin Accessibility Analysis
80	multiomics-rna-atac	Multi-omics Integration (RNA-seq + ATAC-seq)
81	methylation-array-epic	Methylation Array Analysis (Illumina EPIC)

Quick start

# Clone and install
git clone https://github.com/lingzhi227/Extended-BioAgentBench.git
cd Extended-BioAgentBench
pip install click requests

# List tasks
python src/dataset.py list-tasks

# Download a specific task (data + reference + ground truth)
python src/dataset.py download --task outbreak-investigation --reference --results

# Download everything
python src/dataset.py download --all --reference --results

Task format

Each task follows the BioAgentBench format:

tasks/<task_id>/
  Dockerfile          # Reproduce ground truth with this
  environment.yml     # Conda environment specification
  run_script.sh       # Reference pipeline (ground truth generator)

Data, reference, and results are downloaded via dataset.py from HuggingFace:

tasks/<task_id>/
  data/               # Input data (FASTQ, FASTA, etc.)
  reference/          # Reference genomes (if needed)
  results/            # Ground truth output

Evaluation

Each task prompt provides the expected output format (CSV columns + example values). Evaluation uses GPT-5.1 as LLM-as-Judge, scoring:

• steps_completed / steps_to_completion — how many pipeline stages the agent executed
• completion_rate — fraction of the pipeline completed
• results_match — full_match / partial_match / no_match against ground truth

Contributing new tasks

This benchmark is designed to grow. To add a new task:

1. Pick a bioinformatics domain not yet covered
2. Find small public data (< 1 GB, runtime < 4h on 8 CPUs)
3. Write run_script.sh to generate ground truth
4. Write a task prompt that says what to produce, not how
5. Verify the prompt doesn't leak tool names or pipeline structure
6. Submit a PR

Citation

Based on BioAgentBench:

@article{patino2025bioagentbench,
  title={BioAgentBench: A Benchmark for Evaluating LLM Agents in Bioinformatics},
  author={Patino, Luis and others},
  journal={arXiv preprint arXiv:2601.21800},
  year={2025}
}