LMAS Report

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     Last Metagenomic Assembler Standing

Overview

LMAS is an automated workflow enabling the benchmarking of traditional and metagenomic prokaryotic de novo assembly software using defined mock communities. The results are presented in an interactive HTML report where selected global and reference specific performance metrics can be explored.

This repo contains the source code for the interactive report that comes pre-packaged with LMAS.

Installation & Use

This project uses npx webpack to compile a standalone main.js file to be integrated into LMAS.

Re-create conda env

The necessary dependencies for the project are provided in the environment.yml file available in this repo.

To recreate it, simply run:

conda env create -f environment.yml

Additionally, the js dependencies need to be installed. Run in the root of the repo:

npm install

Compile main.js

Run in the root of the repo:

npx webpack 

This creates the main.js in the dist/ directory where the command was run. It expects the index.html file in the same location, created by the LMAS workflow.

Citation and Contacts

LMAS is developed at the Molecular Microbiology and Infection Unit (UMMI) at the Instituto de Medicina Molecular Joao Antunes, in collaboration with Microbiology, Advanced Genomics and Infection Control Applications Laboratory (MAGICAL) at the Faculty of Health Sciences, Ben-Gurion University of the Negev.

This project is licensed under the GPLv3 license.

If you use LMAS please cite LMAS repository.