CELEBRIMBOR: Pangenomes from metagenomes

  1. Joel Hellewell
  2. Samuel T. Horsfield
  3. Johanna von Wachsmann
  4. Tatiana Gurbich
  5. Robert D. Finn
  6. Zamin Iqbal
  7. Leah W. Roberts
  8. John A. Lees
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Abstract

Summary

Metagenome Assembled Genomes (MAGs) are often incomplete, with sequences missing due to errors in assembly or low coverage. Incomplete MAGs present a particular challenge for identification of shared genes within a microbial population, known as core genes, as a core gene missing in only a few assemblies will result in it being mischaracterized at a lower frequency. 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.

Availability and implementation

CELEBRIMBOR is published under open source Apache 2.0 licence at<ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://github.com/bacpop/CELEBRIMBOR">https://github.com/bacpop/CELEBRIMBOR</ext-link>and is available as a Docker container. Supplementary material is available in the online version of the article.

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