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Welcome to the Seqwin documentation.

1. Command Line Parameters
2. Description of Outputs
3. Key Parameters
4. Build and Install from Source
5. FAQs

Tip

Need Help? If you encounter bugs or have feature requests, please open an Issue on our main repository.

Seqwin Architecture Overview

flowchart TD
  CLI["seqwin.cli: app/main"] --> CFG["seqwin.config: Config"]
  CLI --> RUN["seqwin.core: run(config)"]
  RUN --> SEQ["seqwin.core: Seqwin.run()"]
  SEQ --> ASM["seqwin.assemblies: Assemblies / get_assemblies()"]
  ASM --> NCBI-D["seqwin.ncbi: download_taxon()"]
  ASM --> MASH["seqwin.mash: get_jaccard()"]
  SEQ --> KMG["seqwin.kmers: KmerGraph / get_kmers()"]
  KMG --> BTL["seqwin.btllib: indexlr()"]
  BTL --> EXT["C++ extension: _core (pybind11)"]
  SEQ --> MRK["seqwin.markers: ConnectedKmers / get_markers()"]
  MRK --> NCBI-B["seqwin.ncbi: blast()"]

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