CELEBRIMBOR: Core and accessory genes from metagenomes

Joel Hellewell, Samuel T. Horsfield, Johanna Von Wachsmann, Tatiana A. Gurbich, Robert D. Finn, Zamin Iqbal, Leah W. Roberts, John A. Lees

Research output: Contribution to journalArticlepeer-review

Abstract

Motivation: Metagenome-Assembled Genomes (MAGs) or Single-cell Amplified Genomes (SAGs) are often incomplete, with sequences missing due to errors in assembly or low coverage. This presents a particular challenge for the identification of true gene frequencies within a microbial population, as core genes missing in only a few assemblies will be mischaracterized by current pangenome approaches. Results: Here, we present CELEBRIMBOR, a Snakemake pangenome analysis pipeline which uses a measure of genome completeness to automatically adjust the frequency threshold at which core genes are identified, enabling accurate core gene identification in MAGs and SAGs.

Original languageEnglish
Article numberbtae542
JournalBioinformatics
Volume40
Issue number9
Early online date19 Sept 2024
DOIs
Publication statusPublished - 30 Sept 2024

Data Availability Statement

Code for CELEBRIMBOR and pangenome simulations is available on Github (https://github.com/bacpop/CELEBRIMBOR). Code for cgt is also available on Github (https://github.com/bacpop/cgt).

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

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