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Updated: Jun 8, 2025
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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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Removal of sequencing adapter contamination improves microbial genome databases
Andrew H Moeller1, Brian A Dillard2, Samantha L Goldman2
1Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08540, USA. andrew.moeller@princeton.edu.
BMC Genomics
|November 4, 2024
Summary
Sequencing adapter contamination in microbial genome databases reduces assembly quality. Cleaning these contaminated ends improves the accuracy and contiguity of reference genomes for microbiome research.
Area of Science:
- Microbiology
- Genomics
- Bioinformatics
Background:
- Reference genome databases are crucial for microbiome research.
- Advances in genome assembly have expanded these databases.
- Previous studies have not fully addressed contamination issues.
Purpose of the Study:
- To identify and quantify sequencing adapter contamination in microbial genome databases.
- To assess the impact of contamination on genome assembly quality.
- To improve the accuracy and contiguity of reference microbial genomes.
Main Methods:
- Analysis of published microbial genome databases (human, mouse, cow, pig, fish, honeybee, marine).
- Identification and removal of adapter-contaminated sequence ends.
- Reassembly of contaminated genome sequences.
- Quality assessment of improved assemblies.
Main Results:
- Significant sequencing adapter contamination was found across multiple microbial genome databases.
- Contamination systematically reduced genome assembly accuracy and contiguity.
- Removing contaminated ends and reassembling improved the quality of MGnify reference genomes.
Conclusions:
- Sequencing adapter contamination is a pervasive issue in microbial genome databases.
- Addressing contamination is essential for reliable microbiome research.
- The developed method enhances the quality of publicly available microbial genome assemblies.
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