This is the repository for SNAPPy, a Snakemake pipeline for HIV-1 subtyping by phylogenetic pairing. SNAPPy allows high-throughput HIV-1 subtyping locally while being resource efficient and scalable. This pipeline was constructed using Snakemake , and it uses MAFFT and for multiple sequence alignment, BLAST for similarirty querys, IQ-TREE for phylogenetic inference, and several Biopython modules for data parsing an analysis. For in-depth information on how the tool works please visit the documentation page. SNAPPy was design for Linux based operative systems.
In the documentation page you can find a Quick install Guide and an Install point-by-point .
SNAPPy usage is demonstrated in the documentations in SNAPPy commands, furthermnore the Tutorials section coins example on how to use SNAPPy.
Pedro M M Araújo, Joana S Martins, Nuno S Osório, SNAPPy: A snakemake pipeline for scalable HIV-1 subtyping by phylogenetic pairing, Virus Evolution, Volume 5, Issue 2, July 2019, vez050, https://doi.org/10.1093/ve/vez050