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Journal Article

Acanthophis: a comprehensive plant hologenomics pipeline

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Murray,  KD       
Department Molecular Biology, Max Planck Institute for Biology Tübingen, Max Planck Society;

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Weigel,  D       
Department Molecular Biology, Max Planck Institute for Biology Tübingen, Max Planck Society;

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Citation

Murray, K., Borevitz, J., Weigel, D., & Warthmann, N. (2024). Acanthophis: a comprehensive plant hologenomics pipeline. The Journal of Open Source Software (JOSS), 9(95): 6062. doi:10.21105/joss.06062.


Cite as: https://hdl.handle.net/21.11116/0000-000F-1ED0-5
Abstract
Acanthophis is a comprehensive pipeline for the joint analysis of both host genetic variation
and variation in the composition and abundance of host-associated microbiomes (together,
the “hologenome”). Implemented in Snakemake (Köster & Rahmann, 2012), Acanthophis
handles data from raw FASTQ read files through quality control, alignment of the reads to a
plant reference, variant calling, taxonomic classification and quantification of microbes, and
metagenome analysis. The workflow contains numerous practical optimisations, both to reduce
disk space usage and maximise utilisation of computational resources. Acanthophis is available
under the Mozilla Public Licence v2 at https://github.com/kdm9/Acanthophis as a python
package installable from conda or PyPI (pip install acanthophis).