PaperQA2
Agentic RAG package that answers questions from scientific papers with grounded in-text citations.
About
FutureHouse designed PaperQA2 to answer scientific questions the way a careful researcher would: search a corpus of papers, gather and re-rank evidence with contextual summarization, then compose an answer with grounded in-text citations pointing at specific sources. The agentic loop decides which tools to invoke at each step, and the team's research reports superhuman performance against human experts on scientific question answering, summarization, and contradiction detection benchmarks. It installs as pip install paper-qa on Python 3.11 or newer, offering both a pqa command-line interface and a Python API, and the project switched to calendar versioning in December 2025 as development continues. Model access goes through LiteLLM, so OpenAI, Claude, and Gemini models work alongside fully local ones served by Ollama or llama.cpp, with optional Crossref, Unpaywall, and Semantic Scholar keys easing large-scale indexing. The code is Apache-2.0 licensed and the repository has more than 9,000 stars. Research groups and biotech teams embed it wherever literature review needs to be fast, cited, and reproducible.
Should you use PaperQA2?
Pick it when
Use PaperQA2 when a research group or biotech team needs answers from a corpus of scientific papers with in-text citations to specific sources, and wants a CLI or Python API that runs on hosted or local models.
Look elsewhere when
Skip it for general business documents or a chat UI for staff; it is tuned for scientific literature and ships as a CLI and Python API. RAGFlow or AnythingLLM fit office files better, and GPT Researcher suits broad web research reports.
Alternatives to PaperQA2
- GPT Researcher
Plans web and local file research and writes long cited reports, broader in sources but less tuned for evidence gathering across papers.
- STORM
Writes Wikipedia-style articles with citations from web search, better for topic overviews than precise questions over a paper set.
- RAGFlow
General RAG engine with chunk-level citations and a web UI, better for mixed business documents than a literature-focused agent.
- FlashRAG
Built for researchers studying RAG methods on benchmarks and needs an 8GB GPU, not for answering questions from your own paper library.
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Details
- Category
- RAG & Document Retrieval
- Price
- Free
- Platform
- Local/Desktop
- Difficulty
- Easy (2/5)
- License
- Apache-2.0
- Added
- Jul 29, 2026