Getting started

Installation

git clone https://github.com/bioforensics/yeat.git
cd yeat
conda env create -f environment.yml
conda create -n yeat-velvet -c bioconda "perl-velvetoptimiser>=2.2" -y
conda activate yeat

# Linux only; Bandage and MetaMDBG must be installed manually on macOS
conda install -c bioconda "bandage>=0.8" "metamdbg>=1.0" -y

pip install .

Further Installation Instructions for Non-Linux Users

Users on operating systems other than Linux (e.g., macOS) will need to manually install some packages, as not all dependencies are available via Anaconda. Follow the manual installation guide for macOS for detailed instructions.

Usage

yeat-auto {sample names} --seq-path {path to dir with Fastq files} > config.cfg
# Check and edit config.cfg before proceeding
yeat --outdir {path} config.cfg

Run a simple YEAT job without a configuration file for paired-end reads only:

just-yeat-it --outdir {path} {short_read1} {short_read2}