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Automated ensemble assembly and validation of microbial genomes
Sergey Koren1, Todd J Treangen, Christopher M Hill
1National Biodefense Analysis and Countermeasures Center, 110 Thomas Johnson Drive, Frederick, MD 21702, USA. korens@nbacc.net.
BMC Bioinformatics
|June 3, 2014
Summary
iMetAMOS automates genome assembly and validation, providing multiple high-quality, validated assemblies for researchers. This ensemble approach simplifies selecting the best genome assembly for specific analyses.
Area of Science:
- Bioinformatics
- Genomics
- Computational Biology
Background:
- Democratization of DNA sequencing necessitates improved genome assembly and validation methods.
- Individual labs increasingly perform genome sequencing, requiring standardized best practices.
- Previous evaluations show no single best genome assembly approach; multiple assemblies require validation.
Purpose of the Study:
- To present iMetAMOS, an automated ensemble assembly pipeline.
- To streamline the process of running, validating, and selecting genome assemblies.
- To encourage community adoption of best practices in genome assembly.
Main Methods:
- iMetAMOS integrates multiple leading open-source assemblers into a single binary.
- Automated parameter selection and execution of multiple assemblers.
- Scoring assemblies using multiple validation metrics and annotating for genes/contaminants.
Main Results:
- iMetAMOS reliably produces validated genome assemblies and identifies contamination.
- Demonstrated utility on 225 Mycobacterium tuberculosis genomes and a Rhodobacter sphaeroides dataset.
- Intelligent parameter selection yielded R. sphaeroides assemblies comparable to or exceeding GAGE-B evaluation quality.
Conclusions:
- Ensemble assembly with iMetAMOS offers multiple, validated assemblies per genome.
- The approach is effective and reproducible for generating high-quality assemblies.
- Enables users to select the most suitable assembly for their specific research needs.
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