Getting started

Installation

git clone https://github.com/bioforensics/yeat.git
cd yeat
conda env create -f environment.yml
conda activate yeat
pip install .

# Create separate environment for verkko
conda create -n yeat-verkko "verkko>=2.2" pulp=2.7 python=3.11

MacOS

# Install myloasm from the source into the yeat environment
git clone https://github.com/bluenote-1577/myloasm --recurse-submodules  
cd myloasm
cargo build --release
cp target/release/myloasm $CONDA_PREFIX/bin/

# Create separate environment for megahit
conda create -n yeat-megahit "megahit=1.2.9=hfbae3c0_0"  

Linux

# Install myloasm directly into the yeat environment
conda install "myloasm>=0.2"

# Create separate environment for megahit
conda create -n yeat-megahit "megahit>=1.2"

Usage

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

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

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