InsertionMapper

InsertionMapper identifies targeted sequences in multidimensional high-throughput sequencing (HTS) data to assign insertion sites and support reverse genetics analyses such as mapping transposon Ds insertions in maize.

Key Features:

• Modular Architecture: Structured into independent modules addressing preprocessing, database modeling, dimension deconvolution, and element mapping.
• Data Preprocessing: Performs quality checks and formatting of raw sequencing reads.
• Database Modeling: Constructs a database model to organize and manage sequence information.
• Dimension Deconvolution: Deciphers multidimensional pooling strategies to attribute sequences to their respective samples or targets.
• Element Mapping: Maps identified sequences back to specific genomic elements or insertion sites.
• NGS Short-Read Handling: Processes extensive short-read output generated by next-generation/high-throughput DNA sequencers.
• Adjustable Parameters: Offers configurable parameters and settings tailored to experimental designs.
• Validation: Supports validation of identified sequences using PCR assays.

Scientific Applications:

• Reverse Genetics (maize Ds insertions): Applied to sequence-indexing approximately 15,000 independent insertions of the transposon Ds in maize in the "New reverse genetics resources for maize" project.
• Targeted Sequencing across Large Sample Sets: Enables identification of specific genomic regions across numerous samples using multidimensional pooling.
• Functional Genomics and Complex Experimental Designs: Facilitates analysis of pooled sequencing experiments by deconvoluting multidimensional data to assign targets and samples.

Methodology:

Computational steps comprise data preprocessing (quality checks and formatting), database modeling, dimension deconvolution of multidimensional pooling, and mapping of sequences to genomic elements or insertion sites.