paper-reader

paper-reader is a skill for Claude Code from KhaledSaeed18/dotclaude. It costs 92 tokens per session (848 once invoked), scanned A, original, MIT.

A structured way to read one research paper from a PDF, arXiv record, DOI, or text. It records the paper's claim, method, evidence, limitations, relevance, and quotations with page or section locations.

In plain words
What is it for?
Use it to make consistent notes for a literature review, check what a study actually shows, and collect accurately located quotations.
Why use it?
It prevents summaries from relying only on an abstract and makes later claims traceable back to the paper.

Skill for Claude Code

Written for Claude Code: argument-hint in frontmatter.

Part of the thesis plugin — 21 skills, 3 commands, 2 agents shipped together

Good fit Use it to make consistent notes for a literature review, check what a study actually shows, and collect accurately located quotations.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/khaledsaeed18/dotclaude/paper-reader
Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent
npx skills add KhaledSaeed18/dotclaude --skill paper-reader
Clone the repo
git clone --depth 1 https://github.com/KhaledSaeed18/dotclaude

Made for: Claude Code.

Or install thesis, the plugin that ships this one along with the rest of its 21 skills, 3 commands, 2 agents.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for paper-reader

README.md
[![agentmods](https://agentmods.dev/badge/skills/khaledsaeed18/dotclaude/paper-reader/github.svg)](https://agentmods.dev/skills/khaledsaeed18/dotclaude/paper-reader)
Your own site
<a href="https://agentmods.dev/skills/khaledsaeed18/dotclaude/paper-reader"><img src="https://agentmods.dev/badge/skills/khaledsaeed18/dotclaude/paper-reader/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

agentmods 80×15 button for paper-reader

Your own site · 80×15
<a href="https://agentmods.dev/skills/khaledsaeed18/dotclaude/paper-reader"><img src="https://agentmods.dev/badge/skills/khaledsaeed18/dotclaude/paper-reader.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 92 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 848 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.
Origin original No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5.1 $0.00092 $0.00848
Opus 5.5 $0.00037 $0.00339
Sonnet 5.5 $0.00018 $0.00170
Haiku 4.5 $0.00009 $0.00085

Measured 25d ago against content hash ff7dc7ffee2e, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

paper-reader scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 25d ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

.claude-plugin/plugins/thesis/skills/paper-reader/SKILL.md · 74 lines

How it starts

The opening of the file, as written. The whole thing — 74 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Read the paper, not the abstract. The note you produce will be trusted later, when the student is writing under deadline and will not reopen the PDF, so every claim in the note must be traceable to a page or section.

Get the text

  • A local PDF: extract text (pdftotext -layout file.pdf -), and read the figures and tables where the text is unclear.
  • An arXiv id: fetch the LaTeX source when available (https://arxiv.org/e-print/<id>, a gzipped tar) because it keeps equations and tables intact; otherwise the PDF (https://arxiv.org/pdf/<id>).
  • A DOI: resolve it to metadata with CrossRef, then ask the student for the PDF if it is not open access. Do not summarise a paper from its abstract and pretend it was read.

Read in this order

  1. Abstract, introduction, conclusion: what the authors claim.
  2. Method and setup: what they did, precisely enough to judge the claim.
  3. Results, including tables: what the evidence shows, including what it does not show.
  4. Related work and limitations: where they place themselves and what they concede.
  5. References: which works they lean on (candidates for citation-graph).

The note

Write one markdown file per paper under research/notes/, named <firstauthor><year>-<short-title>.md, with the BibTeX key in the front matter so citation-verifier and lit-review-synthesis can join them:

---
key: smith2023feedback
title: ...
authors: ...
year: 2023
venue: ...
doi: 10.xxxx/yyyy
type: empirical | design | survey | theory | position
read: 2026-09-21
relevance: high | medium | low
---

## One-sentence claim
What the paper says it shows, in your words.

## Research question it answers
Their question, and which of the student's sub-questions it bears on.

## Method
Design, data (source, size), procedure, metrics, baselines. Enough to judge validity.

## Evidence
The key results with numbers, and the table or figure each comes from (Table 3, Fig. 2).
What was not tested.

## Limitations
Theirs (from the paper) and yours (what you noticed).

## Relation to this thesis
Supports / contradicts / extends / provides method for: which claim of the student's, and how.

## Quotable
> "exact sentence" (p. 4, Sec. 3.2)
At most five. Exact text, with location, for use in the review.

## Follow-up
References worth chasing, with the reason.

Read the full file on GitHub · 74 lines

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 25d ago First seen · 74 lines · 92 tokens per session scan A ff7dc7ffee2e

Subscribe to this mod's changes

paper-reader is a skill published in the GitHub repository KhaledSaeed18/dotclaude (5 stars, last pushed 2d ago), licensed MIT. It adds 92 tokens to every session and 848 once invoked, about $0.0004 per session on Opus 5.5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-22.

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