Script to design core genome phylogeny using bacterial genome assemblies

ProkEvo - an automated, reproducible, and scalable framework for high-throughput bacterial population genomics analyses.

Reproducible and comprehensive sequence analyses for single-species bacterial dataset

DELEAT is a bioinformatic analysis pipeline for the design of large-scale genome deletions in bacterial genomes.

An alignment-free deep-learning model trained to classify human gut bacteria

Analyzes the GC skew of bacterial chromosomes using multiple calculations. Outputs a data frame of GC skew values and wiggle files for visualization.

Variant barcoding pipeline using single nucleotide polymorphisms (SNPs) for the generation of M. orygis standardised markers for diagnostic and epidemiological use.

Pipeline for de novo assembly of bacterial genomes from paired-end Illumina reads

Python scripts that predict and plot the location of the origin of replication (oriC) of circular bacterial genomes based on Z-curve analysis, GC-skew analysis. and certain gene locations

Various scripts I used during my tenure as a Postdoctoral Associate at Cornell University

A Bash script that automates the search in bacterial genomes for LuxR and LuxI -like proteins. These are important components for Quorum Sensing in bacteria

A snakemake workflow for regions of difference discovery in Mycobacterium tuberculosis complex (MTBC) samples

Computer vision in the service of bacteriology refers to the use of computer algorithms and technology to analyze and interpret images of bacteria for the purpose of identifying and characterizing different types of bacteria.

Bacterial plasmid annotation pipeline

Origin of Chromosomal Replication Assessment. Python tool for the analysis of circular bacterial DNA sequences in order to find their origin of replication.

Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).

The CGView Comparison Tool (CCT) is a package for visually comparing bacterial, plasmid, chloroplast, and mitochondrial sequences.

A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences

A nextflow pipeline for performing bacterial RNA-Seq data analysis.