CELEBRIMBOR: core and accessory genes from metagenomes

Area of Science:

• Microbial genomics
• Bioinformatics
• Computational biology

Background:

• Metagenome-Assembled Genomes (MAGs) and Single-cell Amplified Genomes (SAGs) often suffer from incompleteness due to assembly errors or low coverage.
• This incompleteness challenges accurate identification of gene frequencies in microbial populations.
• Current pangenome methods mischaracterize core genes when they are missing in only a few genome assemblies.

Purpose of the Study:

• To develop a robust pangenome analysis pipeline for identifying core genes in incomplete MAGs and SAGs.
• To address the limitations of current pangenome approaches in handling fragmented genomic data.
• To enable accurate gene frequency determination in microbial populations represented by MAGs and SAGs.

Main Methods:

• Introduction of CELEBRIMBOR, a Snakemake-based pangenome analysis pipeline.
• Implementation of a genome completeness measure to dynamically adjust core gene identification thresholds.
• Utilizing Snakemake for reproducible and scalable pangenome analysis.

Main Results:

• CELEBRIMBOR accurately identifies core genes even in incomplete MAGs and SAGs.
• The pipeline automatically adjusts frequency thresholds based on genome completeness, overcoming limitations of fixed thresholds.
• Improved characterization of gene frequencies in microbial populations derived from fragmented genomes.

Conclusions:

• CELEBRIMBOR provides an accurate method for core gene identification in pangenome analyses of MAGs and SAGs.
• The pipeline enhances the reliability of microbial population gene frequency estimations.
• CELEBRIMBOR is an open-source tool available for broader application in microbial genomics.