gdtools_check

gdtools_check identifies and characterizes structural variations in microbial genomes using Genome Diff inputs, breseq-derived split-read alignments from DNA resequencing data, and statistical evaluation of read coverage evenness.

Key Features:

• Structural Variation Detection: Identifies deletions, insertions, and transposon activities by using split-read alignments to pinpoint new sequence junctions, including junctions involving repeat sequences.
• Statistical Modeling: Employs a statistical model that evaluates read coverage evenness to distinguish true structural variations from false positives and supports reliable predictions at modest genome coverage (>40-fold).
• Genome Diff-based Mutation Application: Accepts a single Genome Diff and multiple reference files and applies mutations from the Genome Diff to reference sequences.
• Reference Genome Integration: Requires a closely related reference genome to describe predicted mutations and their effects on genes.
• Output Generation: Produces comprehensive output files containing all references in the requested format with detailed mutation descriptions and gene-effect annotations.

Scientific Applications:

• Microbial Epidemiology: Detection of transposon insertions and large-scale chromosomal changes to study genetic bases of outbreaks and resistance mechanisms.
• Experimental Evolution: Tracking spontaneous structural mutations over time to analyze evolutionary dynamics in controlled experiments.
• Synthetic Biology: Identification of unintended genomic alterations to support design and maintenance of engineered microbial genomes.
• Genetics Research: Uncovering structural genetic variations that contribute to phenotypic changes in microbes.

Methodology:

Uses breseq-derived split-read alignments from DNA resequencing to detect new sequence junctions (including repeats), employs a statistical model to evaluate read coverage evenness, takes a single Genome Diff and multiple reference files as input, applies mutations from the Genome Diff to the reference sequences, and outputs comprehensive files listing all references with detailed mutation and gene-effect annotations.