Arafat Rahman

This study compares short- and long-read sequencing for microbial pathogen genomics, finding that long reads provide more complete assemblies and that variant calling accuracy can be achieved with short-read pipelines when long reads are fragmented.

The paper identifies two natural isolates of Agrobacterium tumefaciens with fused chromosomes, revealing constraints for replicon fusion and survival.

Beav is a bacterial genome annotation pipeline that integrates multiple tools and custom models to annotate genes, mobile elements, and regulatory features, producing a comprehensive output.

This paper introduces a model for k-mer frequency change based on a birth-death-migration process to estimate maximum likelihood phylogenies without sequence alignment.