pipesnake: Generalized software for the assembly and analysis of phylogenomic datasets from conserved genomic loci.

MOTIVATION: Phylogenetics has moved into the era of genomics, incorporating enormous volumes of data to study questions at both shallow and deep scales. With this increase in information, phylogeneticists need new tools and skills to manipulate and analyze these data. To facilitate these tasks and encourage reproducibility, the community is increasingly moving towards automated workflows.

RESULTS: Here we present pipesnake, a phylogenomics pipeline written in Nextflow for the processing, assembly, and phylogenetic estimation of genomic data from short-read sequences. pipesnake is an easy to use and efficient software package designed for this next era in phylogenetics.

AVAILABILITY: pipesnake is publicly available on GitHub at https://github.com/AusARG/pipesnake and accompanied by documentation and a wiki/tutorial.

SUPPLEMENTARY INFORMATION: Written in Nextflow, the pipeline is containerized and deployable via Docker, Singularity, and Conda making it easy to run on different compute infrastructures.