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Computer Protocols

Sequencing

.. toctree::
    :maxdepth: 1

    sequencing/sequencing-demultiplex-a-run
    sequencing/sequencing-fix-incorrect-demultiplexing

Assembly

.. toctree::
    :maxdepth: 1

    assembly/assembly-with-itero
    assembly/assembly-with-supernova
    assembly/assembly-with-canu
    assembly/assembly-scaffolding-with-arks-and-links
    assembly/polishing-with-pilon

Analysis

.. toctree::
    :maxdepth: 1

    analysis/analysis-cactus
    analysis/analysis-paup
    analysis/analysis-pasta
    analysis/analysis-pargenes
    analysis/analysis-raxml-ng
    analysis/analysis-iq-tree
    analysis/analysis-SVD-quartets
    analysis/analysis-three-rad
    analysis/analysis-radcap
    analysis/analysis-gatk-parallel


Snippets

.. toctree::
    :maxdepth: 1

    snippets/random-computer-snippets
    snippets/make-hpc-bash-better
    snippets/add-new-local-user
    snippets/download-genomes-from-ncbi

Compilation/Installation

.. toctree::
    :maxdepth: 1

    compilation/compiling-iq-tree
    compilation/compiling-pargenes
    compilation/compiling-raxml-ng
    compilation/compiling-canu
    compilation/compiling-arks-and-links
    compilation/installing-supernova

Website

.. toctree::
    :maxdepth: 1

    website/setting-up-personal-websites