ASOkai

User Guide

  • Installation
    • With Conda
    • Windows
    • Verify
  • Getting started
    • Configure a run
    • See what is available
    • Preview before running
    • Run it
    • Run one step or task
    • Override configuration per run
    • Export instead of running
    • Next steps
  • Running the pipeline
    • Configuring runs in YAML
    • Resources
    • Output reuse
    • Configuring runs on the command line
    • Configuring task runs
    • Connecting inputs
    • Exporting a run
  • Analyses

Pipeline Reference

  • Steps
    • Core steps
      • Download genome
      • Create target gene
      • Generate therapeutic candidates
    • Analysis steps
      • Compute intrinsic features
    • Utility steps
      • Build KMC index
      • Build Bowtie 2 index
  • Tasks
    • Find repeated sites
      • Run this task
      • Steps
    • Instantiate target gene
      • Run this task
      • Steps
    • Core tasks
    • Analysis tasks
    • Utility tasks
  • Workflows
    • Standard workflow
      • Run this workflow
      • Direct members
      • Expanded steps

API Reference

  • Analysis
    • Base analysis
      • Analysis
    • Per-unit analyses
      • PerUnitAnalysis
      • IntrinsicFeaturesAnalysis
      • Similar sequences
    • Batch analyses
      • BatchAnalysis
  • Antisense
    • Therapeutics
      • Oligonucleotide
      • AntisenseTherapeutic
      • ASO
      • Gapmer
      • siRNA
    • Candidate design
      • Candidate generation
      • Binding
  • Biochemistry
    • Chemistry
      • Chemistry
    • Mechanisms of action
      • MechanismOfAction
  • Sites
    • Site types
      • Site
      • GenomicSite
      • TranscriptSite
  • Targets
    • Target genes
      • TargetGene
    • Target construction
      • create_target_gene()
  • Types
    • AnalysisUnitType
    • Scalar
    • Strand
    • TargetRegion
  • Utils
    • KMC utilities
      • Imports
      • Running KMC
      • Pipeline integration
      • Running kmc_tools
      • KMC API
      • kmc_tools API
    • Bowtie 2 utilities
      • Bowtie2
      • Bowtie2Build
      • Bowtie2Inspect
      • Bowtie2ExecutionError
      • ReferenceSequence
      • write_reference_fasta()
    • Serialization
      • Serializable

Contributor Guide

  • Adding an analysis step
    • What you are building
    • Before you start
    • Step 1: choose your two base classes
      • Decision 1: how your calculation consumes units
      • Decision 2: what your step writes
    • What each base class gives you
      • The analysis classes
      • The step classes
    • Step 2: write the analysis class
      • Running in parallel
    • Step 3: write the step class
    • Step 4: connect inputs and outputs
      • Taking a file from another step
      • Taking a file from anywhere
      • Declaring what you write
      • Choosing file types
    • Step 5: parameters and configuration
    • Step 6: register and document
    • Step 7: write tests
    • Step 8: check your work
    • Worked example: an output that is not a CSV
    • The template
    • Generated reference documentation
      • Conditional parameter alternatives
    • Publishing a plugin instead
  • Pipeline components
    • Component hierarchy
    • Analysis execution models
    • The step specification
      • Scalar parameters
      • Composing task runs
      • File contracts
      • Output destinations and input configuration
    • Shared step lifecycle
      • Step logging
      • Generated-output validation receipts
    • Analysis-step lifecycle
    • Validation boundaries
  • Internal steps
    • Built-in internal steps
      • Identify potential repeated sites

Project Info

  • License
  • Contributors
ASOkai
  • Utils
  • Edit on GitHub

Utils

Utilities are grouped by responsibility. Choose a section for its usage guide and public Python API.

  • KMC utilities
    • Imports
    • Running KMC
    • Pipeline integration
    • Running kmc_tools
    • KMC API
    • kmc_tools API
  • Bowtie 2 utilities
    • Bowtie2
    • Bowtie2Build
    • Bowtie2Inspect
    • Bowtie2ExecutionError
    • ReferenceSequence
    • write_reference_fasta()
  • Serialization
    • Serializable
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© Copyright 2026, Alexander Schliep. Last updated on 2026-10-12.

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