Exact mapping of Illumina blind spots in the genome reveals platform-wide and workflow-specific biases.

Whole-genome sequencing (WGS) is fundamental to basic research and many clinical applications. Coverage across Illumina-sequenced genomes is known to vary with sequence context, but this bias is poorly characterized. Here, through a novel application of phylogenomics that distinguishes genuine coverage bias from deletions, we discern Illumina 'blind spots' in the reference genome for seven sequencing workflows.

Drivers and sites of diversity in the DNA adenine methylomes of 93 complex clinical isolates.

This study assembles DNA adenine methylomes for 93 complex (MTBC) isolates from seven lineages paired with fully-annotated, finished, de novo assembled genomes. Integrative analysis yielded four key results. First, methyltransferase allele-methylome mapping corrected methyltransferase variant effects previously obscured by reference-based variant calling.