Robert A. Petit III, PhD rpetit3

Sequence-based typing is critical for microbial genomics, yet existing tools are often developed in isolation, leading to duplicated effort, inconsistent formats, and limited community participation.

Computational analysis of large-scale metagenomics sequencing datasets provides valuable isolate-level taxonomic and functional insights from complex microbial communities.

We have adopted an open bioinformatics ecosystem to address the challenges of bioinformatics implementation in public health laboratories (PHLs).

We report comparisons between WGS and DNA metabarcoding for plant species identification.

Convert various bioinformatic outputs to TSV

Generate basic stats for an assembly

A Python package for working with Bactopia

A WDL wrapper around Bactopia

Classification through YAML Heuristic Mapping Protocol

Assemble bacterial isolate genomes from Nanopore reads