Rules
=====
- Reference

  - Alignment

    .. toctree::
      reference/alignment/summary.rst

  - Report

    - Comparison

      .. toctree::
        reference/report/comparison/summary.rst

    - Phylogenetic Tree

      .. toctree::
        reference/report/phylogenetic_tree/summary.rst

  - Download

    .. toctree::
      reference/download/summary.rst

  - Attributes

    - Desc

      .. toctree::
        reference/attributes/desc/summary.rst

  - Index

    - Dict

      .. toctree::
        reference/index/dict/summary.rst

    - Fai

      .. toctree::
        reference/index/fai/summary.rst

  - Phylogeny

    .. toctree::
      reference/phylogeny/summary.rst

- Assembly

  - Report

    - Quality Report

      .. toctree::
        assembly/report/quality_report/summary.rst

    - Assembly Graph

      .. toctree::
        assembly/report/assembly_graph/summary.rst

  - Assembler

    .. toctree::
      assembly/assembler/summary.rst

- Variant

  - Report

    - Calling

      .. toctree::
        variant/report/calling/summary.rst

    - Summary

      .. toctree::
        variant/report/summary/summary.rst

  - Caller

    .. toctree::
      variant/caller/summary.rst

- Mapping

  - Postprocess

    - Deduplicated

      .. toctree::
        mapping/postprocess/deduplicated/summary.rst

    - Realigned

      .. toctree::
        mapping/postprocess/realigned/summary.rst

    - Read Group

      .. toctree::
        mapping/postprocess/read_group/summary.rst

    - Sorted

      .. toctree::
        mapping/postprocess/sorted/summary.rst

    - Deoverlapped

      .. toctree::
        mapping/postprocess/deoverlapped/summary.rst

    - Filtered

      .. toctree::
        mapping/postprocess/filtered/summary.rst

  - Merged

    .. toctree::
      mapping/merged/summary.rst

  - Mapper

    .. toctree::
      mapping/mapper/summary.rst

    - Indices

      .. toctree::
        mapping/mapper/indices/summary.rst

  - Report

    - Quality Report

      .. toctree::
        mapping/report/quality_report/summary.rst

    - Methylation

      .. toctree::
        mapping/report/methylation/summary.rst

  - Index

    .. toctree::
      mapping/index/summary.rst

- Reads

  - Report

    - Quality Report

      .. toctree::
        reads/report/quality_report/summary.rst

  - Preprocess

    - Decontaminated

      .. toctree::
        reads/preprocess/decontaminated/summary.rst

    - Deduplicated

      .. toctree::
        reads/preprocess/deduplicated/summary.rst

    - Subsampled

      .. toctree::
        reads/preprocess/subsampled/summary.rst

    - Joined

      .. toctree::
        reads/preprocess/joined/summary.rst

    - Trimmed

      .. toctree::
        reads/preprocess/trimmed/summary.rst

  - Conversion

    .. toctree::
      reads/conversion/summary.rst

- Classification

  - Transcripts

    .. toctree::
      classification/transcripts/summary.rst

  - Report

    - Taxonomic Counts

      - Barplot

        .. toctree::
          classification/report/taxonomic_counts/barplot/summary.rst

      - Count Table

        .. toctree::
          classification/report/taxonomic_counts/count_table/summary.rst

      - Pieplot

        .. toctree::
          classification/report/taxonomic_counts/pieplot/summary.rst

      - Alpha Diversity

        .. toctree::
          classification/report/taxonomic_counts/alpha_diversity/summary.rst

    - Transcripts

      - Pca

        .. toctree::
          classification/report/transcripts/pca/summary.rst

      - Revigo

        .. toctree::
          classification/report/transcripts/revigo/summary.rst

      - Count Table

        .. toctree::
          classification/report/transcripts/count_table/summary.rst

      - Html Table

        .. toctree::
          classification/report/transcripts/html_table/summary.rst

    - Summary

      .. toctree::
        classification/report/summary/summary.rst

  - Read Based

    .. toctree::
      classification/read_based/summary.rst

  - Viral

    .. toctree::
      classification/viral/summary.rst

    - Identification

      .. toctree::
        classification/viral/identification/summary.rst

  - Contig Based

    .. toctree::
      classification/contig_based/summary.rst

  - Differential Analysis

    .. toctree::
      classification/differential_analysis/summary.rst

    - Filter Significant

      .. toctree::
        classification/differential_analysis/filter_significant/summary.rst


