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Assessing genome assembly quality prior to downstream analysis: N50 versus BUSCO
April A Jauhal1,2, Richard D Newcomb2
1School of Biological Sciences, University of Auckland, Auckland, New Zealand.
Molecular Ecology Resources
|February 25, 2021
Summary
Genome assembly quality is complex. The N50 score doesn't always predict gene completeness (BUSCO scores), highlighting the need for diverse quality metrics in genomic research.
Area of Science:
- Genomics
- Bioinformatics
- Comparative Genomics
Background:
- Publicly available eukaryotic genome assemblies are increasing.
- Genome quality is often oversimplified to a single metric, like N50.
- N50 may not correlate with other essential quality dimensions.
Purpose of the Study:
- To evaluate if the N50 score reliably predicts gene space completeness.
- To compare N50 and Benchmarking Universal Single-Copy Orthologs (BUSCO) scores across eukaryotic genome assemblies.
Main Methods:
- Meta-analysis of 611 published eukaryotic genome studies.
- Collected N50 and BUSCO scores from the literature.
- Statistical analysis to assess the correlation between N50 and BUSCO scores.
Main Results:
- High N50 scores generally correlated with high BUSCO scores.
- High BUSCO scores were achievable even with low N50 scores.
- Variations in BUSCO scores with poor N50 may relate to intron number in conserved genes.
Conclusions:
- N50 is not a sufficient proxy for all genome assembly quality aspects, particularly gene space completeness.
- Emphasize the importance of using multiple metrics for genome quality assessment.
- Suggest further investigation into BUSCO score variations and potential improvements for gene space evaluation.
