Comparison

BaseSpace vs Zotero

Price, ratings, monetisation and update history for both apps, side by side — with what reviewers say about each.

Head to head
About

BaseSpace

Monitor your sequencing Runs and Analyses from anywhere. Receive push notifications for completion and track the status of your projects with key metrics and charts.

Highlights
  • Real-time progress monitoring
  • Push notifications for completion
  • Status tracking for Runs and Analyses
  • View metrics and SAV charts
  • Detailed analysis status
Features
Read full description

Easily monitor the progress of your BaseSpace sequencing Runs and Analyses from anywhere. - Get push notifications the moment they are complete - Monitor the status of Runs including metrics & SAV charts - View the detailed status of Analyses

About

Zotero

This research tool helps you collect, organize, annotate, cite, and share your academic and professional work. Save articles, books, and webpages, add notes and highlights, and generate bibliographies in thousands of styles. Collaborate with others and sync your library across devices.

Highlights
  • Collect research from various sources
  • Organize with collections and tags
  • Annotate PDFs and webpages
  • Generate citations and bibliographies
  • Collaborate in group libraries
  • Sync across devices
Features
Read full description

Zotero is a free, easy-to-use research tool that helps you collect, organize, annotate, cite, and share your work. COLLECT • Save journal articles, newspaper articles, books, webpages, and more via the Share button in Safari and other apps • Automatically download article PDFs to read • Quickly add physical books and articles to your Zotero library by scanning book barcodes or article DOIs with your iPhone or iPad camera ORGANIZE • Use collections and tags to organize your research • View and edit bibliographic information for your research items ANNOTATE • Read PDFs, EPUBs, and webpage snapshots and add highlights and notes, or use an Apple Pencil to make freehand annotations CITE • Instantly generate citations and bibliographies in over 10,000 formats and journal styles including APA, Chicago, IEEE, MLA, Turabian, and Vancouver SHARE • Collaboratively collect sources and mark up PDFs in group libraries with your colleagues • Synchronize your personal and group research libraries to access them via Zotero’s desktop app and the Zotero website • Use the Zotero desktop app to insert your annotations into Word, LibreOffice, and Google Docs documents and automatically generate bibliographies from the sources you used Visit zotero.org to learn more about everything you can do with Zotero. Having trouble? Have an idea? Post bug reports and feature requests to the Zotero Forums at forums.zotero.org to talk directly to Zotero developers. ZOTERO AND PRIVACY Since 2006, the Zotero team has been committed to creating the best research software, and we believe that includes putting you in full control of your own work. We’re an independent, nonprofit organization, and we’ll never sell your data.

Screenshots

BaseSpace4 screens
Zotero2 screens

Verdict

The call

The clearest difference is review sentiment: Zotero at 78% against BaseSpace's 25%. Zotero also leads on rating (4.6 vs 2.7) and ratings volume (435 vs 12). BaseSpace's advantage is iOS requirement (8.0 vs 16.6). On price, ads, in-app purchases and monetization model there is nothing between them.

Scored on Price · Rating · Positive reviews · Number of ratings · Update frequency · Ads · In-app purchases · Monetization · Best chart rank · Devices · Requires iOS

CostPrice · In-app purchases · Ads · Monetization

Both are free to download. Neither carries in-app purchases, so what you see is what you pay.

ReceptionRating · Positive reviews · Number of ratings

Zotero holds the better App Store score, 4.6 against 2.7. That said, the two scores are not equally well evidenced: Zotero has 435 ratings behind it against 12, so its average is the more settled of the two. Written reviews point the same way: 25% of BaseSpace's written reviews are positive against 78% of Zotero's.

UpkeepUpdate frequency

BaseSpace ships an update every 2 months, Zotero every 3 weeks. The most recent releases landed on October 20, 2026 and October 27, 2026 respectively.

Scorecard5 real differences · 5 level
BaseSpace versus Zotero: the parameters behind the verdict, then further details
ParameterBaseSpaceZotero
PriceFreeFree
Rating2.7 (12 ratings)4.6 (435 ratings) — better
Positive reviews25.0% of reviews77.9% of reviews — better
Number of ratings12435 — better
Update frequencyEvery 2 monthsEvery 3 weeks — better
AdsNoNo
In-app purchasesNoNo
MonetizationFreeFree
DevicesiPhone, iPodiPhone, iPad
Requires iOS8.0 — better16.6
Further details — not scored
Size11 MB237 MB
Age rating4+4+
DeveloperIllumina, Inc.Zotero

Customer experience

BaseSpace

All ratings12 ratings
Positive33.3%
Neutral16.7%
Negative50.0%
Written reviews8 reviews
Positive25.0%
Neutral12.5%
Negative62.5%

Zotero

All ratings431 ratings
Positive89.6%
Neutral4.9%
Negative5.6%
Written reviews263 reviews
Positive77.9%
Neutral10.3%
Negative11.8%

Bugs and requests

BaseSpace

Not enough reviews yet to summarise bugs or requests.

Zotero

Reported bugs

4 issues
  • Unable to unzip PDF snapshots
  • Annotations disappearing or moving unexpectedly
  • Dark mode not working as expected
  • Inability to add citations directly from the app

Requested features

6 requests
  • Eraser tool for annotations
  • More color options for pen and highlighter
  • Ability to open PDFs in external apps
  • Bookmarking and table of contents support
  • Improved search functionality
Show 1 more
  • Offline access to downloaded PDFs

In-app purchases

None

BaseSpace

No in-app purchases

None

Zotero

No in-app purchases

Questions

Is BaseSpace free?
BaseSpace is free to download, with no in-app purchases.
Is Zotero free?
Zotero is free to download, with no in-app purchases.
Which has better reviews, BaseSpace or Zotero?
Zotero is rated higher. BaseSpace averages 2.7 out of 5 from 12 ratings, while Zotero averages 4.6 from 435 ratings.
Do BaseSpace or Zotero have ads?
Neither BaseSpace nor Zotero shows ads.
Which is updated more often, BaseSpace or Zotero?
BaseSpace ships an update every 2 months, and Zotero every 3 weeks. Most recently, BaseSpace was updated on October 20, 2026 and Zotero on October 27, 2026.

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