PaperQuay is more than a PDF reader or a Zotero add-on. It is a local-first desktop literature manager designed for students, researchers, and paper writers who want to manage papers, read PDFs, annotate, translate, screen papers quickly, and use AI agents without leaving the same workspace.
Many paper tools force the user to choose between fragmented workflows: one app for PDF reading, another tool for translation, another chat window for paper summaries, and another library manager for metadata. PaperQuay combines these into a single desktop workflow while keeping Zotero compatibility optional rather than mandatory.
PaperQuay — AI-Assisted Literature Management That Keeps Reading Flow Intact
PaperQuay is more than a PDF reader or a Zotero add-on. It is a local-first desktop literature manager designed for students, researchers, and paper writers who want to manage papers, read PDFs, annotate, translate, screen papers quickly, and use AI agents without leaving the same workspace.
Many paper tools force the user to choose between fragmented workflows: one app for PDF reading, another tool for translation, another chat window for paper summaries, and another library manager for metadata. PaperQuay combines these into a single desktop workflow while keeping Zotero compatibility optional rather than mandatory.
Research workflow problem
Traditional tools
PaperQuay
Translation latency interrupts reading
Translate only after selecting text, often with visible API delay
Pre-translate MinerU structural blocks and jump instantly to cached translations
Side-by-side translation hurts focus
Two columns require constant eye movement and can break formatting
Keep the original PDF visible while navigating to precise translated blocks on demand
Pure translated files lose source context
Original wording, terminology, and academic expression are hidden
Keep source text, parsed blocks, translation, notes, and overview linked together
Fast paper screening is repetitive
Upload PDFs to an LLM one by one and manually organize outputs
Generate and store structured paper overviews inside the local library
AI model choices are locked down
Built-in models or platform-specific token pricing
Bring your own OpenAI-compatible endpoint, model, and runtime parameters
Large libraries are hard to clean
Manual renaming, tagging, metadata fixes, and classification
Agent tools can assist with batch rename, metadata completion, tagging, and classification
Zotero migration is inconvenient
Either stay locked in Zotero or rebuild everything manually
Import Zotero collections, tags, and PDF attachments as an optional source
What Makes PaperQuay Different
Live workflow demo: browse the library, open papers, inspect structured reading, and move into the Agent workspace without leaving the same desktop flow.
Instant Block-Level Translation
PaperQuay uses a translation workflow designed for long paper reading sessions. It can translate and cache MinerU-parsed structural blocks in advance. Later, when reading, clicking a source block can instantly jump to its translated counterpart. Translation no longer needs to happen only after each click or selection.
Fast Paper Screening from the Overview Panel
PaperQuay is designed not only for deep reading, but also for screening large numbers of papers quickly. In the overview panel, each paper can directly surface AI-generated fields such as background, research question, method, experiment setup, key findings, conclusions, and limitations. This allows you to judge whether a paper deserves deeper reading directly inside the library workflow before opening the full PDF in detail.
Literature Library, Not Just Import
PaperQuay can build an independent local library with PDF import, a configurable storage folder, categories, tags, metadata editing, search, filtering, notes, and SQLite-based local persistence. Zotero remains supported as an optional import source, not a required dependency.
Agent Operations for Paper Management
The agent workspace is designed for library operations, not just conversation. It can assist with batch renaming, metadata completion, smart tagging, tag cleanup, automatic classification, and paper summarization while exposing tool calls and results for user review.
Core Workflow
Step
What happens
1. Import PDFs
Drag PDFs into the app or choose files from the import dialog.
Rust commands for files, SQLite, Zotero import, MinerU, metadata, translation, overview, QA, and agent operations
src-tauri/
Tauri v2 configuration, icons, installer assets, and Rust crate
Requirements
Node.js 18 or newer
Rust stable toolchain
Platform requirements for Tauri v2 on your OS
Windows, macOS, or Linux
Optional external services:
MinerU API key for cloud PDF structure parsing.
OpenAI-compatible API key for paper overviews, translation, QA, and agent tasks.
Internet access for Crossref metadata enrichment.
Development
Install dependencies:
npm install
Start the desktop app in development mode:
npm run tauri:dev
Build the frontend only:
npm run build
Check the Rust host:
cd src-tauri
cargo check
Build the desktop installer:
npm run tauri:build
Zotero Compatibility
PaperQuay can read a local Zotero data directory that contains zotero.sqlite. During import it copies the Zotero database to a temporary read-only working file and does not modify your original Zotero database.
Imported data enters PaperQuay's own local literature library. Zotero collections become local categories, and available local PDFs inside those collections are copied into the PaperQuay paper storage folder.
Zotero is an optional compatibility source, not a required dependency. You can build a complete library directly inside PaperQuay without using Zotero.
Data and Privacy
PaperQuay is local-first. The literature database is stored as SQLite, and imported PDFs are stored in the paper storage folder you configure.
Do not commit local data, API keys, PDFs, parser outputs, or backups. The .gitignore excludes common local runtime folders, SQLite databases, API key files, build output, backup archives, and private PDFs by default.
Roadmap
Better metadata extraction from PDF first pages.
DOI / arXiv / Semantic Scholar enrichment options.
More advanced PDF annotations and export.
Citation style generation.
Database backup and restore UI.
Folder watching for automatic import queues.
RAG-based knowledge-base QA.
One-click survey generation and Word / LaTeX research draft generation.
Optional cloud sync after the local-first model is stable.
Acknowledgements
PaperQuay is also shaped by discussions, feedback, and shared ideas from the LinuxDo community.
License
PaperQuay Community Edition is licensed under AGPL-3.0-only.
If you distribute modified versions or provide modified versions over a network, keep the license and copyright notices, mark your changes, and provide the corresponding source code under AGPL terms. For closed-source commercial licensing, commercial support, or brand-name permission, contact the maintainer separately. See TRADEMARKS.md for brand-use notes.
