Home

Introduction

• About - What does FACET do and how does it do it?

Installation

• Dependencies - What does FACET need to run?

• Installation - How do I install FACET once I have the dependencies installed? Work in progress

Usage

• Quick Start - For the impatient; Offers abridged explanations for running modules with links to more detailed explanations. Work in progress

• Module Overview - What each module is, plus how and when to use them

  • Database - An in-depth explanation of the Database Module

  • Database-free - An in-depth explanation of the database-free module

  • Outfile - An in-depth explanation of the outfile module

  • Masker - An in-depth explanation of the masker module

  • Variant Call - An in-depth explanation of the vcf module

• Neat applications - Some novel applications of FACET that wouldn't initially jump out at users

Output Formats

• CSV - Work in progress

• GFF - Work in progress

• SAM/BAM - Work in progress

• TIC - TIg Coverage file; A newly developed file format for compactly storing alignment information; Work in progress

Examples

• Searching a fungal genome for three transposons using the database module

• Searching a fungal genome for three transposons using the database-free module

• Searching a fungal genome for three transposons using the outfile module

• Masking a fungal genome

• Finding false SNP calls in a fungal genome Work in progress