SkewIT

SkewIT computes a single-metric quantification of GC skew in bacterial genomes to enable large-scale analysis of replication-associated nucleotide asymmetry and detection of potential mis-assemblies in complete genome sets such as NCBI RefSeq.

Key Features:

• GC skew quantification: Computes a single metric representing the degree of GC skew across bacterial genomes.
• Phylogenetic signal: Reveals conserved GC skew patterns within phyla such as Firmicutes and distinct patterns in Actinobacteria.
• Mis-assembly detection: Flags genomes with outlier skew metric values indicative of potential assembly errors.
• Large-scale analysis: Enables analysis across thousands of complete bacterial genomes, including over 15,000 sequences in NCBI RefSeq.

Scientific Applications:

• Genomic Quality Control: Identification of mis-assembled chromosomal sequences by detecting outlier GC skew metrics.
• Evolutionary Biology: Exploration of conserved and divergent GC skew patterns to inform evolutionary relationships among bacteria.
• Comparative Genomics: Large-scale analysis of genome structure and replication-associated nucleotide asymmetry across many bacterial genomes.

Methodology:

Calculates a single metric that summarizes genome-wide GC skew to permit efficient comparative analysis across thousands of genomes.