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