Brian Bushnell

The paper analyzes CRISPR spacers from metagenomic data to reveal patterns of CRISPR targeting across Earth's biomes, identifying selection pressures and non-host phage interactions.

QuickBin is a CPU-native metagenome binning tool that produces high-fidelity MAGs efficiently, outperforming existing methods in recovery and contamination control.

DynamicDemiLog (DDL) is a unified sketch that estimates cardinality, similarity, frequency, and composition efficiently, outperforming existing methods in speed and accuracy.

GradeBins provides a framework to assess metagenomic bin quality by evaluating complete bin sets with per-bin and bin-set summaries, supporting both inference and ground truth modes.

RandomReadsMG simulates realistic metagenomes for benchmarking and AI/ML training, offering faster performance and accurate depth distribution modeling.

The paper compares sequence search tools for detecting CRISPR spacer-target interactions and finds significant differences in their performance.

The paper describes a metagenome processing workflow that includes assembly, annotation, and binning, and provides tools for researchers to apply it to their data.