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Research · head to head

DNAnexus vs Paperpile

DNAnexus logo

DNAnexus

Research

Regulated cloud platform for genomic and multiomic data, with GxP and FedRAMP coverage

From
On request
Rated
-
Full reviewWebsite
Paperpile logo

Paperpile

Research

Reference management essentials

From
$4.15/month
Rated
-
Full reviewWebsite

The short version

  • Each has a real cost: DNAnexus no pricing is published, so an organisation cannot compare the total cost against running the same pipelines on its own cloud account until it is deep in a sales process.; Paperpile no monthly billing option; annual billing only
  • Prices and features above were last checked on 31 August 2026.

Where they differ

Only the attributes on which DNAnexus and Paperpile actually diverge.

Attributes where DNAnexus and Paperpile differ
AttributeDNAnexusPaperpile
Starting priceOn request$4.15/month
Pricing modelquotesubscription
PlatformsWeb, LinuxWeb

Identical on both: free tier (No), user rating (Not yet rated), category (Research).

What each one covers

Drawn from each product's published feature list. An absence here means we hold no record of it - not that the product lacks it.

Only in DNAnexus

  • Governed data storage
  • Workflow execution
  • App building
  • Controlled collaboration
  • Compliance posture
  • Cohort browsing

Only in Paperpile

Nothing recorded that DNAnexus does not also cover.

What people use each for

The jobs each tool is most often brought in to do.

DNAnexus

  • A clinical diagnostics laboratory that needs a CLIA and CAP aligned environment for production sequencing pipelines without building the compliance evidence itselfnot Paperpile
  • A pharma sponsor analysing genomic endpoints in a registrational programme where 21 CFR Part 11 records are requirednot Paperpile
  • A biobank or consortium giving hundreds of external researchers governed access to a dataset too large to distributenot Paperpile
  • A diagnostics vendor packaging its pipeline as a versioned app so partner laboratories can run it without receiving the source codenot Paperpile

Paperpile

  • Organizing research papers and managing academic citationsnot DNAnexus
  • Creating citations in multiple styles and BibTeX for writingnot DNAnexus
  • Collaborating on research through shared reference librariesnot DNAnexus
  • Integrating citations into Google Docs and Microsoft Wordnot DNAnexus

Where each one falls short

Documented limitations, not opinions. Every one is a constraint you would hit in normal use.

DNAnexus

  • No pricing is published, so an organisation cannot compare the total cost against running the same pipelines on its own cloud account until it is deep in a sales process.
  • Compute and storage are billed through the platform rather than at underlying cloud list price, so the compliance envelope carries a persistent margin on every terabyte and core hour, which grows with the science rather than staying fixed.
  • Data egress at genomic scale is slow and chargeable, so leaving the platform later is a real project rather than a contract decision, and that gravity weakens negotiating position at renewal.
  • The regulated and validated configurations sit in a higher commercial tier than the research configuration, so an organisation that starts in research mode and later needs GxP faces a repricing rather than a setting change.
  • Bioinformaticians used to running Nextflow on their own infrastructure find the platform abstractions constraining, and porting an existing pipeline into the app model is engineering work that does not carry over to any other platform.

Paperpile

  • No monthly billing option; annual billing only
  • Regular plan lacks full-text PDF search and annotations
  • Safari and Firefox browser extensions currently in beta
  • Chrome signup initially required

Pricing, plan by plan

DNAnexus

On request
  • DNAnexus Platform$undefined/year
    • Quoted per organisation through a sales process
    • Storage and compute billed through the platform rather than at cloud list price
    • Regulated and validated configurations are a separate commercial tier

Paperpile

$4.15/month
  • Regular$4.15/month
    • Basic reference management
    • PDF storage and citation generation
    • Integrations with Word, Google Docs, and academic databases
  • Expert$5.75/month
    • All Regular features
    • Full-text PDF search
    • Notes and annotations

Which should you pick?

Choose DNAnexus if

  • You need governed data storage.
  • You work on Web, Linux.
  • You also want workflow execution.
DNAnexus review

Choose Paperpile if

Nothing in the data separates Paperpile from DNAnexus on the points above - pick on price and on how each one feels to use.

Paperpile review

Questions people ask

Is DNAnexus or Paperpile better?
Neither clearly leads. DNAnexus starts at On request and Paperpile at $4.15/month, and user ratings are close enough to be indistinguishable. Choose on capability and platform support.
Which is cheaper, DNAnexus or Paperpile?
DNAnexus starts at On request and Paperpile at $4.15/month.
Does DNAnexus or Paperpile run on more platforms?
DNAnexus runs on Web, Linux. Paperpile runs on Web.
What is DNAnexus best used for?
DNAnexus is most often used for a clinical diagnostics laboratory that needs a clia and cap aligned environment for production sequencing pipelines without building the compliance evidence itself, a pharma sponsor analysing genomic endpoints in a registrational programme where 21 cfr part 11 records are required, a biobank or consortium giving hundreds of external researchers governed access to a dataset too large to distribute, a diagnostics vendor packaging its pipeline as a versioned app so partner laboratories can run it without receiving the source code. Of those, a clinical diagnostics laboratory that needs a clia and cap aligned environment for production sequencing pipelines without building the compliance evidence itself and a pharma sponsor analysing genomic endpoints in a registrational programme where 21 cfr part 11 records are required are not what Paperpile is typically brought in for.
What can DNAnexus do that Paperpile cannot?
DNAnexus covers Governed data storage, Workflow execution, App building, Controlled collaboration.

Answered from the vendors’ own pages

DNAnexus: Why pay for DNAnexus instead of raw AWS?

For the compliance evidence. GxP, FedRAMP, CLIA, CAP and Part 11 coverage removes a validation programme most organisations would otherwise have to build and maintain themselves.

Paperpile: How much does Paperpile cost?

Paperpile costs $4.15 per month for the Regular plan or $5.75 per month for the Expert plan, both billed annually.

Source
DNAnexus: Is validated use included?

No. Regulated and validated configurations sit in a separate commercial tier from ordinary research use.

Paperpile: Is there a free trial available for Paperpile?

Yes, Paperpile offers a 30-day free trial for both plans.

Source
DNAnexus: Can I get my data out?

Yes, but egress at genomic scale is chargeable and slow, so plan exit costs at the point of signing.

Paperpile: Does Paperpile offer academic or group discounts?

Yes, students, faculty, and researchers receive 50% off, and group discounts up to 20% off Expert plans are available when purchasing multiple seats.

Source
DNAnexus: Does it host UK Biobank?

Yes, DNAnexus hosts the UK Biobank research analysis platform, which has its own access approval and cost terms.

Paperpile: What billing options does Paperpile offer?

Paperpile accepts credit cards and PayPal, with additional payment options by location. Purchase orders are accepted for Enterprise customers.

Source
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