TIS

TIS analyzes transposon insertion sequencing (TIS) data to map transposon insertion sites and quantify insertion counts across microbial genomes to identify genes influencing phenotypes.

Key Features:

• Comprehensive workflows: Includes data de-multiplexing, promoter sequence identification, transposon flank alignment, and read count repartition across the genome.
• Quality control and optimization: Provides procedures for determining optimal tool parameters and removing contamination to ensure reliable and reproducible results.
• Support for Mariner-based transposon datasets: Handles Mariner-based transposons that are distributed relatively evenly and support high insertion densities (average >30 insertions per kilobase) for saturated-library analyses.
• Standardization and best practices: Synthesizes insights from existing tools and addresses common challenges to propose reliable practices aimed at standardizing TIS methodologies.

Scientific Applications:

• Gene function discovery: Systematically investigate gene function by analyzing the effects of transposon insertions on microbial phenotypes.
• Microbial genomics and pathogen biology: Identify genetic elements that govern biological processes in microbes and pathogens.
• Therapeutic and biotechnological target identification: Inform potential therapeutic strategies and biotechnological applications by pinpointing genes affecting survival and growth.

Methodology:

Computational methods explicitly comprise data de-multiplexing, promoter sequence identification, transposon flank alignment, read count repartition across the genome, determination of optimal analysis parameters, and contamination removal applied to datasets generated with Mariner-based transposons (average >30 insertions per kb) to support saturated-library interpretation.