Acanthophis: a comprehensive plant hologenomics pipeline

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).