Eric Coissac
6acafa7f2c
Introduces a comprehensive documentation set covering theoretical foundations, CLI usage, installation, and system architecture. Adds MkDocs configuration and Makefile targets to generate, serve with live reload, and clean the documentation site. Includes citation styles and bibliography files for academic references.
20 lines
592 B
Markdown
20 lines
592 B
Markdown
# unitig
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Dump the unitigs of an index as FASTA. A unitig is a maximal non-branching path through the de Bruijn graph implied by the index's kmers; the concatenation of every unitig reconstructs every stored kmer exactly once.
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```bash
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obikmer unitig INDEX [OPTIONS]
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```
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## Arguments
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| Argument | Description |
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|---|---|
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| `INDEX` | Index directory |
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## Options
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`unitig` accepts the shared [predicate options](filter.md#predicate-options) (`--ingroup`, `--outgroup`, `--min-count`, etc.) to restrict which kmers are included before the unitigs are enumerated.
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Output is FASTA on stdout.
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