faircloth-lab
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Contents:

  • Lab Protocols
  • Computer Protocols
    • Sequencing
      • Demultiplexing a Sequencing Run
      • Fix Incorrect Demultiplexing
    • Assembly
      • Assembly With Itero
      • Assembly With Supernova
      • Assembly With Canu
      • Assembly Scaffolding With Arks And Links
      • Polishing Assemblies with Pilon
    • Analysis
      • Running Cactus
      • Running PAUP
      • Running Pasta
      • Running Pargenes
      • Running RAxML-NG
      • Running IQ-Tree
      • Running SVD Quartets
      • Running 3RAD Analysis
      • Running RADcap Analysis
      • Running GATK in Parallel
    • Snippets
      • Random Computer Snippets
      • Make a better BASH config
      • Add a new local user
      • Download Genomes From NCBI
    • Compilation/Installation
      • Compiling IQ-tree
      • Compiling Pargenes
      • Compiling RAxML-NG
      • Compiling Canu
      • Compiling Arks And Links
      • Compiling Supernova
    • Website
      • Setting Up Personal Websites
  • Data Protocols
  • Changelog
faircloth-lab
  • Docs »
  • Computer Protocols
  • Edit on GitHub

Computer Protocols¶

Sequencing¶

  • Demultiplexing a Sequencing Run
  • Fix Incorrect Demultiplexing

Assembly¶

  • Assembly With Itero
  • Assembly With Supernova
  • Assembly With Canu
  • Assembly Scaffolding With Arks And Links
  • Polishing Assemblies with Pilon

Analysis¶

  • Running Cactus
  • Running PAUP
  • Running Pasta
  • Running Pargenes
  • Running RAxML-NG
  • Running IQ-Tree
  • Running SVD Quartets
  • Running 3RAD Analysis
  • Running RADcap Analysis
  • Running GATK in Parallel

Snippets¶

  • Random Computer Snippets
  • Make a better BASH config
  • Add a new local user
  • Download Genomes From NCBI

Compilation/Installation¶

  • Compiling IQ-tree
  • Compiling Pargenes
  • Compiling RAxML-NG
  • Compiling Canu
  • Compiling Arks And Links
  • Compiling Supernova

Website¶

  • Setting Up Personal Websites
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© Copyright 2017-2019, Brant Faircloth and The Faircloth Lab Revision e4a8853e.

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