Panalyze: automated virus pangenome variation graph construction and analysis
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Motivation
Constructing and studying reference-free pangenome variation graphs (PVG) can support new insights into viral genomic diversity. Interpreting the information arising from this is challenging, so automating these processes to allow exploratory investigations for optimisation is essential. To address this, we developed an easily deployable pipeline to facilitate the rapid creation of virus pangenome variation graphs that applies a broad range of analyses to these graphs.
Results
We present panalyze, a scalable and unbiased virus pangenome variation graph construction and analysis tool implemented in NextFlow and containerised in Docker. Panalyze avails of NextFlow to efficiently complete tasks across multiple compute nodes and in diverse High-Performance Computing (HPC) environments. We illustrate how Panalyze works and the valuable outputs it can generate using a range of common viral pathogens
Availability
Panalyze is released under a MIT open-source license, available on GitHub with documentation accessible at https://github.com/downingtim/LSDV-PVG/ .
Contact
Chandana.tennakoon@pirbright.ac.uk , tim.downing@pibright.ac.uk
Supplementary information
Supplementary data are available at Bioinformatics online.
