Projects
A few example bioinformatics projects I have developed.
A pipeline to identify any number of Mobile Genetic Elements or other small DNA sequences in an arbitrarily large collection of assembled genomes.
A pipeline to map in vitro CRIPSR spacer acquisition events from Illumina sequence data and visualize against a reference genome.
A pipeline to compare sequence mapping coverage ratios between control and experimental conditions. Allows for the identification of site-specific nuclease cleavage locations.
Additional analyses and visualizations
Poster presentation on building a pipeline for tracking pathogen genomics. Presented at GLBIO 2019 (The International Society for Computational Biology)
Phylogeny of global V cholerae strains with metadata.
Phylogeny of V. cholerae strains from contemporary outbreak.
Pan-genomic comparative analysis of all ICP1 bacteriophage.
Network graph of related V. cholerae phage defense elements.
Global mapping of V. cholerae incidence, colored by defense element types.
Example of bacteriophage comparative genomics showing gene swapping and hybridization.
Example of comparative genomics visualization software from whole genomic alignments.
Screenshot from interactive RNA sequencing viewer software.