Configuration

Basic Usage

If provided a complete or draft microbial reference genome, and one or more sets of reads or BAM files Lorikeet can find variant locations within the reference genome based on the read mappings. Ideally, multiple samples will be provided so log-ratio variances can be calculated between each pairwise combination of variants. If only a single sample is provided, a euclidean distance matrix is calculated based on the abundance of each variant location. Non-negative matrix factorization is then performed on the resulting pairiwse matrix reducing the variants into a lower latent space where each variant is assigned to its resulting dominant factor.

lorikeet genotype -r draft_genome.fasta -1 sample_1.1.fq.gz sample_2.1.fq.gz -2 sample_1.2.fq.gz sample_2.2.fq.gz 

Pygments Options

The following code highlighting options are configured in the config.toml

pygmentsCodeFences = true
pygmentsCodefencesGuessSyntax = true
pygmentsUseClasses = true

Main menu

Configure the main menu by editing the config.toml

[[menu.main]]
name = "Home"
url = "/docs/"
weight = 1

[[menu.main]]
name = "Docs"
url = "/docs/docs/"
weight = 2