LMAS’s

Short-read (meta)genomic assembly: finding the best fit in a world of options.

This is the documentation for LMAS, 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.

In its current form, 10 assemblers are implemented in LMAS, with several steps having been implemented to ensure the transparency and reproducibility of the results with the use of Nextflow and container software.

LMAS is open source and available at https://github.com/cimendes/LMAS

Getting Started

• Overview
• Installation
• About

User Guide

• Basic Usage
• Output and Report
• Short-Read (Meta)Genomic Assemblers
• Parameters
• Metrics

Report

• Overview
• Global Assembly Metrics
• Assembly Metrics per Reference

Developer Guide

• General Orientation
• Add Assembler Process
• Create a Mock Community for LMAS