breseq_bam2aln

breseq_bam2aln identifies structural variations in microbial genomes from DNA resequencing data to characterize new junctions and deleted regions and their impacts on genes.

Key Features:

• Structural Variation Detection: Identifies deletions, insertions, and rearrangements mediated by mobile genetic elements or repetitive sequences by evaluating new sequence junctions with split-read alignments to a reference genome and incorporating matches to repeat sequences.
• Statistical Model Integration: Employs a statistical model of read coverage evenness to validate structural variation predictions and reduce false positives.
• Comprehensive Mutation Descriptions: Combines predicted new junctions and deleted chromosomal regions to produce biologically relevant descriptions of mutations and their effects on genes.
• Performance on Simulations: Demonstrated on simulated Escherichia coli genomes to recover unique breakpoint sequences and mobile element insertions at modest read-depth coverage (>40-fold).

Scientific Applications:

• Microbial Epidemiology: Tracks genomic changes that contribute to pathogenic traits or shifts in microbial lifestyle.
• Experimental Evolution: Identifies spontaneous structural mutations to elucidate the genetic basis of adaptive changes.
• Synthetic Biology and Genetics: Detects unintended genomic alterations in engineered organisms to assess genomic integrity.

Methodology:

Processes high-throughput DNA resequencing data using split-read alignments to a reference genome with explicit matching to repeat sequences, applies a statistical model of read coverage evenness to validate predictions, and combines predicted new junctions and deleted chromosomal regions to describe mutation impacts; performance was evaluated on simulated Escherichia coli genomes at >40-fold coverage.