SNAPPy

SNAPPy performs scalable HIV-1 subtyping by phylogenetic pairing to support molecular epidemiology and evolutionary analyses.

Key Features:

• Scalability and workflow orchestration: Uses Snakemake to manage workflows and leverages multi-core processing to execute phylogenetic inference and BLAST tasks sequentially or in parallel.
• Local processing: Runs on Linux-based systems for local execution of analyses.
• Comprehensive subtyping: Analyzes full-length HIV-1 genomes and partial regions GAG, POL, and ENV and recognizes over ninety circulating recombinant forms (CRFs).
• Phylogenetic pairing subtyping: Assigns subtypes using phylogenetic pairing approaches integrated into the pipeline.
• Integration of established tools: Incorporates MAFFT for multiple sequence alignment, BLAST for similarity searches, IQ-TREE for phylogenetic inference, and Biopython modules for data parsing.
• Alignment capability: Performs extensive HIV-1 sequence alignments as part of its analyses.

Scientific Applications:

• Drug resistance monitoring: Enables sequence-based surveillance of mutations associated with antiretroviral drug resistance.
• Molecular epidemiology: Supports tracking of HIV-1 subtype distribution and transmission networks in population studies.
• Subtype-related pathogenesis studies: Facilitates investigation of subtype-associated differences in disease progression and transmission efficiency.
• Immune evasion and therapeutic outcome research: Aids studies on subtype impacts on immune escape mechanisms and treatment responses.

Methodology:

Workflow orchestration with Snakemake; multiple sequence alignment with MAFFT; similarity searches with BLAST; phylogenetic inference with IQ-TREE; data parsing with Biopython; subtype assignment via phylogenetic pairing; and optional multi-core parallel execution on Linux.