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bioRxiv · 10.1101/2024.07.12.603264

CompareM2 is a genomes-to-report pipeline for comparing microbial genomes

Kobel, C. M.·Aho, V. T. E.·Oeyaas, O.·Noerskov-Lauritsen, N.·Woodcroft, B. J.·Pope, P. B.
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Abstract

Here, we present CompareM2, a genomes-to-report pipeline for comparative analysis of bacterial and archaeal genomes derived from isolates and metagenomic assemblies. CompareM2 is easy to install and operate, and integrates community-adopted tools to perform genome quality control and annotation, taxonomic and functional predictions, as well as comparative analyses of core- and pan-genome partitions and phylogenetic relations. The central results generated via the CompareM2 workflow are emphasized in a portable dynamic report document. CompareM2 is free software and welcomes modifications and pull requests from the community on its Git repository at https://github.com/cmkobel/comparem2.

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Kobel, C. M., Aho, V. T. E., Oeyaas, O., Noerskov-Lauritsen, N., Woodcroft, B. J., Pope, P. B.. 2024-07-16. CompareM2 is a genomes-to-report pipeline for comparing microbial genomes. https://doi.org/10.1101/2024.07.12.603264

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