Comparison
paper-qa vs khoj
Verdict
Pick paper-qa if paperQA2 version 5 is a retrieval-augmented generation (RAG) system optimized for extracting information from scientific documents, enhancing user queries with citations; pick khoj if khoj is a self-hosted AI assistant that supports integration with multiple LLMs, enabling users to build custom agents and conduct deep research using both web and local documents.
Markdown twin · paper-qa alternatives · khoj alternatives
GraphCanon updated Sep 20, 2026
11views this month
Trust & integrity
| Signal | paper-qa | khoj |
|---|---|---|
| Maintenance | Very active (5d since push) As of Aug 18, 2026 · github_public_v1 | Steady (47d since push) As of Sep 18, 2026 · github_public_v1 |
| Provenance | Not a fork · Organization account As of Aug 18, 2026 · github_public_v1 | Not a fork · Organization account As of Sep 18, 2026 · github_public_v1 |
| OSV dependency advisories | No lockfile (source not queried) As of Jul 11, 2026 · osv@v1 | No lockfile (source not queried) As of Sep 18, 2026 · osv@v1 |
| deps.dev advisories | Not queried deps.dev@v1 | Not queried deps.dev@v1 |
| OpenSSF Scorecard | Not queried openssf-scorecard@v1 | Not queried openssf-scorecard@v1 |
Tagline
- paper-qa
- High accuracy RAG for answering questions from scientific documents with citations
- khoj
- Self-hostable AI second brain for personalized research and automation
Stars
- paper-qa
- 9.0k
- khoj
- 37k
Forks
- paper-qa
- 907
- khoj
- 2.5k
Open issues
- paper-qa
- 141
- khoj
- 150
Language
- paper-qa
- Python
- khoj
- Python
Adopt for
- paper-qa
- PaperQA2 version 5 is a retrieval-augmented generation (RAG) system optimized for extracting information from scientific documents, enhancing user queries with citations.
- khoj
- Khoj is a self-hosted AI assistant that supports integration with multiple LLMs, enabling users to build custom agents and conduct deep research using both web and local documents.
Persona
- paper-qa
- -
- khoj
- -
Runtime
- paper-qa
- -
- khoj
- -
License
- paper-qa
- 'Apache-2.0' - Permissive free software license that allows for both non-commercial use and commercial exploitation of the package.
- khoj
- Khoj is licensed under AGPL-3.0, which means it is free to use, modify, and distribute, but any derivative works must also be released under the same license.
Last pushed
- paper-qa
- Aug 12, 2026
- khoj
- Aug 2, 2026
Categories
- paper-qa
- Data & Retrieval, Model Training
- khoj
- AI Agents, Data & Retrieval, Developer Tools, Inference & Serving, Model Training
Trust and health
Maintenance
- paper-qa
- Very active (96%)
- khoj
- Steady (60%)
Days since push
- paper-qa
- 5d
- khoj
- 47d
Open issues (now)
- paper-qa
- 141
- khoj
- 150
Stars delta
- paper-qa
- +154 (30d)
- khoj
- +887 (30d)
Open issues delta
- paper-qa
- 0 (30d)
- khoj
- +17 (30d)
Full report
- paper-qa
- Trust report
- khoj
- Trust report
Typed relationship
paper-qa alternative khojBoth PaperQA2 and khoj are designed to work with documents for question answering, leveraging AI technologies like RAG (Retrieval-Augmented Generation) for high accuracy in scientific literature.
Choose paper-qa if…
- License: paper-qa is Apache-2.0, khoj is AGPL-3.0.
- Requirements: Min 4 GB RAM.
- Both PaperQA2 and khoj are designed to work with documents for question answering, leveraging AI technologies like RAG (Retrieval-Augmented Generation) for high accuracy in scientific literature.
- Tags unique to paper-qa: rag, science, search.
- Your project specifically requires processing and querying scientific documents, as PaperQA2 offers specialized capabilities tuned for this domain.
When NOT to use paper-qa
- If your use case does not involve scientific document processing, another RAG system better suited to your specific type of documents (e.g., legal, medical) might be more fitting.
- In scenarios where real-time performance is critical and extensive indexing or access to external APIs for large-scale paper handling becomes a bottleneck.
Choose khoj if…
- License: khoj is AGPL-3.0, paper-qa is Apache-2.0.
- Pricing: Khoj is free to use, but users may incur costs related to hosting and the LLMs they choose to integrate..
- Requirements: Min 4 GB RAM; Requires Docker; Khoj requires Docker for setup and operation.; Users must have a Python environment and the necessary dependencies installed..
- Both PaperQA2 and khoj are designed to work with documents for question answering, leveraging AI technologies like RAG (Retrieval-Augmented Generation) for high accuracy in scientific literature.
- Tags unique to khoj: agent, assistant, chat, chatgpt.
- Also covers AI Agents, Developer Tools, Inference & Serving.
- khoj ships Docker support for self-hosted deployment.
- When you need a self-hosted solution for personalized research and automation that can integrate with a variety of LLMs, including GPT, Claude, Gemini, LLaMA, Qwen, and Mistral.
When NOT to use khoj
- If you are looking for a cloud-based service without the need for self-hosting, Khoj may not be the best fit.
- Khoj might not be ideal if you are seeking a tool that does not support a wide range of LLMs and requires a more specialized integration.
- If your research and automation needs are simple and do not require deep integration with local documents or web sources, a more straightforward tool might be more appropriate.
Explore
Sources
Every stat on this page traces to a dated GitHub sync, license file, enrichment field, or trust scan.
- GitHub stars (Future-House/paper-qa) · observed Sep 20, 2026
- GitHub forks (Future-House/paper-qa) · observed Sep 20, 2026
- Last push (Future-House/paper-qa) · observed Aug 12, 2026
- License file (Apache-2.0) · observed Sep 20, 2026
- Decision facts (enrichment) · observed Jul 12, 2026
- Trust scan (lockfile / OSV) · observed Jul 11, 2026
- GitHub stars (khoj-ai/khoj) · observed Sep 20, 2026
- GitHub forks (khoj-ai/khoj) · observed Sep 20, 2026
- Last push (khoj-ai/khoj) · observed Aug 2, 2026
- License file (AGPL-3.0) · observed Sep 20, 2026
- Decision facts (enrichment) · observed Sep 18, 2026
- Trust scan (lockfile / OSV) · observed Sep 18, 2026
GitHub stars on cards: paper-qa 9.0k · khoj 37k (synced Sep 20, 2026).
Common questions
- What is the difference between paper-qa and khoj?
- paper-qa: High accuracy RAG for answering questions from scientific documents with citations. khoj: Self-hostable AI second brain for personalized research and automation. See the comparison table for live GitHub stats and shared categories.
- When should I choose paper-qa over khoj?
- Choose paper-qa over khoj when License: paper-qa is Apache-2.0, khoj is AGPL-3.0; Requirements: Min 4 GB RAM; Both PaperQA2 and khoj are designed to work with documents for question answering, leveraging AI technologies like RAG (Retrieval-Augmented Generation) for high accuracy in scientific literature; Tags unique to paper-qa: rag, science, search; Your project specifically requires processing and querying scientific documents, as PaperQA2 offers specialized capabilities tuned for this domain.
- When should I choose khoj over paper-qa?
- Choose khoj over paper-qa when License: khoj is AGPL-3.0, paper-qa is Apache-2.0; Pricing: Khoj is free to use, but users may incur costs related to hosting and the LLMs they choose to integrate.; Requirements: Min 4 GB RAM; Requires Docker; Khoj requires Docker for setup and operation.; Users must have a Python environment and the necessary dependencies installed.; Both PaperQA2 and khoj are designed to work with documents for question answering, leveraging AI technologies like RAG (Retrieval-Augmented Generation) for high accuracy in scientific literature; Tags unique to khoj: agent, assistant, chat, chatgpt; Also covers AI Agents, Developer Tools, Inference & Serving; khoj ships Docker support for self-hosted deployment; When you need a self-hosted solution for personalized research and automation that can integrate with a variety of LLMs, including GPT, Claude, Gemini, LLaMA, Qwen, and Mistral.
- When should I avoid paper-qa?
- If your use case does not involve scientific document processing, another RAG system better suited to your specific type of documents (e.g., legal, medical) might be more fitting. In scenarios where real-time performance is critical and extensive indexing or access to external APIs for large-scale paper handling becomes a bottleneck.
- When should I avoid khoj?
- If you are looking for a cloud-based service without the need for self-hosting, Khoj may not be the best fit. Khoj might not be ideal if you are seeking a tool that does not support a wide range of LLMs and requires a more specialized integration. If your research and automation needs are simple and do not require deep integration with local documents or web sources, a more straightforward tool might be more appropriate.
- Is paper-qa or khoj more popular on GitHub?
- khoj has more GitHub stars (37,399 vs 9,048). Stars measure visibility, not whether either tool fits your constraints.
- Are paper-qa and khoj open source?
- Yes - both are open-source projects on GitHub (paper-qa: Apache-2.0, khoj: AGPL-3.0).
- Where can I find alternatives to paper-qa or khoj?
- GraphCanon lists graph-backed alternatives at paper-qa alternatives and khoj alternatives (paper-qa markdown twin, khoj markdown twin), ranked by typed relationship edges rather than popularity votes.
- Is there a machine-readable version of this comparison?
- Yes. The markdown twin at this comparison mirrors this page for agents and LLM crawlers, with the same stats table and FAQ answers.
- Which is better maintained, paper-qa or khoj?
- paper-qa: Very active. khoj: Steady. Compare maintenance labels, days since push, and release cadence in the trust section below - stars alone do not measure maintenance.
- Where are the full trust reports for paper-qa and khoj?
- GraphCanon publishes per-repo trust reports with dated maintenance, provenance, and scan summaries: paper-qa trust report; khoj trust report.