CELEBRIMBOR: core and accessory genes from metagenomes.

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.

Availability and implementation

CELEBRIMBOR is published under open source Apache 2.0 licence at https://github.com

SUBMITTER: Hellewell J 

PROVIDER: S-EPMC11422503 | biostudies-literature | 2024 Sep

REPOSITORIES: biostudies-literature