The Code Ocean Apps Library

Ready-to-use Biotech Applications Speed Up Your Discovery Efforts

Code Ocean Apps Library

With Code Ocean’s Apps Library, you get code-free access to more than 30 pre-vetted, ready-to-use applications addressing popular biotech and life sciences topics, including:

  • Genomics
  • Variant Calling
  • Single Cell
  • And more…

What You Get

  • 30+ pre-built and pre-vetted applications, all ready-to-use
  • Applications can be used as-is, or customized based on user needs
  • New applications are continually added to the Apps Library
  • Ongoing customer support for applications available in the Apps Library

Available Applications

Code Ocean Apps Library contains applications relating to many fields of biotechnology. These are just some of the available applications Code Ocean customers get instant access to:


  • Delly Germline complete analysis
  • Delly Somatic complete analysis
  • FeatureCounts
  • GATK RNAseq short variant discovery
  • MacS3 Peak Calling
  • Smoove complete analysis

Bulk Sequencing

  • BWA
  • BWA Index
  • BWA-MEM2
  • Bowtie2
  • Bowtie2 Index
  • BWA-MEM2-Index
  • Salmon
  • STAR
  • STAR Index


  • Fastp
  • Sambamba – Filter
  • Sambamba – Remove Duplicates
  • Trim Galore


  • ColabFold: AlphaFold2
  • FastQC
  • Fetch Data with FFQ
  • Img2Mol
  • MLFlow (orchestration using S3)
  • MultiQC
  • Tensorboard GPU
  • DECIMER 2.0

Want to see the Code Ocean Apps Library in Action?

Watch our on-demand webinar: Breaking Barriers: Speed Up Time To Your Next Scientific Breakthrough

Schedule a Demo Today

Want to see the applications in the Apps Library for yourself?

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