Overview

Metahit is a cutting-edge metagenomic data processing pipeline.

System Requirements

Hardware requirements

Metahit requires only a x86 computer with enough RAM (64GB+ is recommended) to support the in-memory operations.

OS Requirements

Metahit is supported and tested in Linux systems only.

Software Setup

Run bash setup.sh to install external dependenceies. Run conda env create -f env.yaml in root directory Run conda activate metahit_env to activate conda env. RUN conda env remove -n metahit_env to delete env Then, in the conda environment, directly run bash demo.sh and the pipeline will be triggered.

Database setup

The folder (db_setup) contains three scripts to download and set up databases for CheckM, CheckM2, and GTDB-Tk. By default, each script downloads the database into a database folder in your current working directory. You can optionally provide a custom path.

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• CheckM database downloading: checkm_db.sh

  bash db_setup/checkm_db.sh [DB_DIR]

• CheckM2 database downloading: checkm2_db.sh

  bash db_setup/checkm2_db.sh [DB_DIR]

• GTDB-TK database downloading: tdbtk_db.sh

  bash db_setup/gtdbtk_db.sh [DB_DIR] [RELEASE_VERSION]

  Example:

  bash db_setup/gtdbtk_db.sh /your/custom/path 214

Usage

A demo

bash demo.sh

Contacts

Hang Yu([email protected])