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bioRxiv · 10.1101/2024.04.05.588231

CELEBRIMBOR: Pangenomes from metagenomes

Hellewell, J.·Horsfield, S. T.·von Wachsmann, J.·Gurbich, T.·Finn, R. D.·Iqbal, Z.·Roberts, L. W.·Lees, J.
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Abstract

SummaryMetagenome 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 implementationCELEBRIMBOR is published under open source Apache 2.0 licence at https://github.com/bacpop/CELEBRIMBOR and is available as a Docker container. Supplementary material is available in the online version of the article.

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Hellewell, J., Horsfield, S. T., von Wachsmann, J., Gurbich, T., Finn, R. D., Iqbal, Z., Roberts, L. W., Lees, J.. 2024-04-09. CELEBRIMBOR: Pangenomes from metagenomes. https://doi.org/10.1101/2024.04.05.588231

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