Comparing and Evaluating Metagenome Assembly Tools from a Microbiologist's Perspective - Not Only Size Matters!

Area of Science:

• Microbiology
• Bioinformatics
• Computational Biology

Background:

• Next Generation Sequencing (NGS) and metagenomics are vital for studying microbial communities.
• Increasing data output from metagenomics presents computational and bioinformatics challenges.
• A wide array of software tools exists, but selecting appropriate ones is difficult, especially for non-bioinformaticians.

Purpose of the Study:

• To assess common, freely available metagenome assembly tools.
• To provide a guide for the microbiological community on tool selection.
• To evaluate tools based on output statistics, sensitivity, community profile variability, and ease-of-use.

Main Methods:

• Tested publicly available metagenome assembly tools on real Illumina sequencing data.
• Used natural microbial communities from forest soil and algal biofilms of varying complexity.
• Compared assemblers on metrics including output statistics, sensitivity for low-abundance members, and phylogenetic profile reliability.

Main Results:

• Different assembly tools are optimal depending on sample type, computational resources, and research objectives.
• Performance varied across tested assemblers when applied to diverse natural microbial communities.
• Detailed insights into tool principles, pitfalls, user-friendliness, and reliability were generated.

Conclusions:

• Tool selection in metagenomics requires careful consideration of specific research needs and data characteristics.
• This assessment provides practical guidance for microbiologists navigating the landscape of metagenome assembly software.
• Understanding tool limitations and strengths is key to reliable microbial community profiling.