Episode 142: Microbinfie - genomeqc

In this episode of the microbinfie podcast, Nabil-Fareed Alikhan introduces GenomeQC, a comprehensive approach to establishing species-specific genome quality control thresholds for bacterial genomics.

Errata: The project name was changed to qualibact and is no longer genomeqc as mentioned on the episode. See more at the Qualibact website

Key Points

1. Genome Quality Assessment

• Addresses the challenge of determining genome assembly quality metrics
• Provides species-specific thresholds for genome size, contig count, and other parameters
• Helps researchers understand what constitutes a 'good' genome assembly

2. Data and Methodology

• Leverages 1.2 million bacterial genome assemblies for analysis
• Uses Illumina-based assemblies as primary reference
• Computationally lightweight, taking only half a day to process on a compute cluster

3. Future Development

• Plans to create a command-line tool with traffic light-style quality reporting
• Aims to make thresholds easily implementable in various bioinformatics pipelines
• Open to expanding analysis to different taxonomic levels

Take-Home Messages

• Genome quality assessment requires nuanced, species-specific approaches
• Existing guidelines for genome metrics are often informal and inconsistent
• Standardized thresholds can help researchers quickly assess genome assembly quality