vsgseq2

vsgseq2 analyzes VSGSeq data to enable surveillance of population-wide diversity and abundance of expressed variant surface glycoproteins (VSGs) in Trypanosoma brucei.

Key Features:

• Nextflow Implementation: The workflow is implemented in Nextflow for full reproducibility.
• Transcript Assembly and Quantification: Integrates modern tools for transcript assembly and quantification.
• Computational Efficiency: Improves computational efficiency compared to previous approaches.
• VSG Repertoire Reconstruction: Accurately reconstructs population-wide VSG repertoires from defined expression datasets.
• VSG Expression Proportion Estimation: Better recapitulates VSG expression proportions through benchmarking.
• Enhanced Reproducibility: Improves reproducibility and data utilisation for in vivo infection analyses.

Scientific Applications:

• Parasite Dynamics Research: Enables study of parasite dynamics through analysis of VSG expression patterns.
• Tissue Tropism Investigation: Supports understanding of tissue tropism in Trypanosoma brucei infections.
• Infection Persistence Studies: Facilitates research on mechanisms of infection persistence and chronic infections.
• Immune Evasion Mechanism Analysis: Helps researchers understand mechanisms driving immune evasion in T. brucei.
• Mosaic VSG Analysis: Enables analysis of mosaic VSGs assembled from distinct incomplete VSG gene copies.

Methodology:

vsgseq2 is implemented in Nextflow and integrates modern tools for transcript assembly and quantification. Benchmarking was performed against defined T. brucei VSG expression datasets.