Vertically transmitted microbe detection from unaligned sequencing reads

This repository contains scripts for detecting potentially vertically transmitted microbes in wild strains of C. elegans, C. tropicalis, and C. briggsae using Kraken2 to taxonomically classify DNA from unaligned sequencing reads.

The scripts to perform each analysis

Build Kraken2 database:

scripts/kraken/databaseBuild.sh

Control analysis with microsporidia-infected strains (positive control) and non-infected strains (negative control):

scripts/kraken/kraken_control_analysis.sh

Kraken2 analysis on wild strains of self-fertilizing Caenorhabditis species:

scripts/kraken/kraken_wild_strains.sh

Filtering Kraken2 output

scripts/kraken/wild_strain_kraken_filtering.sh

Creating heatmap figure

scripts/figure/heatmap.R