atavide lite documentation

atavide_lite is a modular metagenomics workflow for quality control, optional host-read removal, read-based taxonomic and functional profiling, assembly, and recovery of metagenome-assembled genomes (MAGs). It supports paired-end short reads and single-end or long reads on Slurm- and PBS-managed high-performance computing (HPC) systems.

The project deliberately uses visible, independently submitted batch scripts instead of hiding the entire analysis inside one workflow invocation. That makes failures easier to locate, individual stages easier to repeat, and CPU, memory, wall-time, storage, and GPU requests easier to tune for each cluster.

Where to begin

New users should follow this path:

Read Overview to decide whether the workflow fits the analysis.
Follow Installation to clone the repository, build its utilities, and create the software environments.
Use Choosing a profile to select scripts for the read type and HPC system.
Complete Quick start with a small, non-sensitive dataset.
Refer to Configuration and Pipeline stages while scaling up.

Cluster maintainers and contributors can start with Contributing and Adding a cluster.

Introduction

User guide

Project links

The documentation describes the repository as shipped. Cluster policies and third-party software change independently, so confirm scheduler limits and software versions with the relevant HPC provider before submitting expensive jobs.