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Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples
Published on: December 22, 2014
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SEQ2MGS: an effective tool for generating realistic artificial metagenomes from the existing sequencing data
Pieter-Jan Van Camp1, Aleksey Porollo2
1Department of Biomedical Informatics, University of Cincinnati, Cincinnati, OH, USA.
NAR Genomics and Bioinformatics
|July 28, 2022
Summary
We created SEQ2MGS, a tool generating artificial metagenomes from real sequencing data. This aids in evaluating bioinformatics tools for metagenomics analysis, especially for complex or understudied microbial communities.
Area of Science:
- Bioinformatics
- Metagenomics
- Genomics
Background:
- Accurate assessment of bioinformatics tools for metagenomics analysis requires realistic benchmark datasets.
- Existing simulation methods may not fully capture the complexity of real-world metagenomic samples.
Purpose of the Study:
- To develop an effective and simple generator of artificial metagenomes from real sequencing experiments.
- To provide a tool that aids in the evaluation of metagenomics analysis pipelines.
Main Methods:
- SEQ2MGS analyzes FASTQ files, precomputes genomic content, and blends shotgun reads from different isolates.
- The tool can spike isolates into real metagenomes in desired proportions, eliminating the need to simulate sequencing variations.
- It supports the generation of complex samples, including those with new or understudied organisms, even without assembled genomes.
Main Results:
- SEQ2MGS was demonstrated to be easy to use for simulating altered Schaedler flora (ASF), comparable to Grinder and CAMISIM.
- When emulating pathogen emergence in the human gut microbiome, common metagenomics tools showed inconsistent results for the background microbiome.
- The MG-RAST platform confirmed that SEQ2MGS accurately transfers genomic information, enabling correct identification of antimicrobial resistance genes.
Conclusions:
- SEQ2MGS offers a practical solution for generating realistic artificial metagenomes, crucial for benchmarking bioinformatics tools.
- The tool simplifies the creation of complex metagenomic samples, facilitating research on diverse microbial communities.
- SEQ2MGS aids in the reliable assessment of metagenomics analysis pipelines, including the detection of functional genes like antimicrobial resistance genes.
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