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User guide

  • Installation
    • External dependencies
    • Reference FASTAs
  • Quick start
    • Terminal UI
    • Programmatic API
  • Pipeline overview
    • Stages
  • Configuration
    • Key parameters
    • Inputs
    • Outputs

Reference

  • API reference
    • Top-level
      • capellini.config
      • capellini.pipeline
    • Stages
      • capellini.stages.preflight
      • capellini.stages.dada2
      • capellini.stages.ncbi_mapping
      • capellini.stages.mmseqs2
      • capellini.stages.spacepharer
      • capellini.stages.procs
      • capellini.stages.network
    • Utilities
      • capellini.utils.io
      • capellini.utils.taxonomy
      • capellini.utils.transforms
      • capellini.utils.network_utils

About

  • Citation
CAPELLINI
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© Copyright 2026, Daniele Pugno, Alexander Dell'Orti, Viet Tran, Christian L. Müller.

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