biotradis

biotradis processes TraDIS (Transposon Directed Insertion Sequencing) transposon insertion sequencing (TIS) data to map insertions from Illumina sequencing and infer gene essentiality, function, and genetic interactions in transposon mutant libraries.

Key Features:

• Extensible Perl library: Implemented as a flexible Perl library that can be extended to develop additional analytical functionality.
• TraDIS and TIS protocol support: Supports TraDIS (Transposon Directed Insertion Sequencing) and other transposon insertion sequencing protocols that produce compatible data formats.
• Insertion mapping and analysis: Maps transposon insertions across genomes and analyzes insertion profiles to infer gene essentiality and genetic interactions.
• Library preparation and sequencing support: Supports TraDIS-specific high-yield library preparation and Illumina sequencing protocols used to generate TIS reads.

Scientific Applications:

• Gene essentiality profiling: Identify essential genes by analyzing transposon insertion absence or depletion across the genome.
• Gene function inference: Associate disruption patterns with phenotypes to infer gene function in functional genomics studies.
• Genetic interaction analysis: Characterize genetic interactions by comparing insertion fitness and patterns between conditions or strains.
• Large-library analysis: Analyze large libraries of isogenic transposon mutants for genome-wide fitness and genotype–phenotype mapping.

Methodology:

Implemented as a Perl library, biotradis performs processing, mapping of Illumina TraDIS reads to genomes, and analysis of transposon insertion sites and insertion profiles.