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

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

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

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

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

bacterial mategnomes assembly and pangenomes

Medium scale identification of genomic neighbors in bacterial genomes

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

Bacterial plasmid annotation pipeline

Snakemake workflow for bacterial genome assembly + polishing for Oxford Nanopore (ONT) sequencing using multiple tools.

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

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

🦠💻Operational taxonomic units calculation with abundance greedy clustering🧬🔄

domain analyzer for analyzing interpro domains

metegnome sequence extractions from MAGs

Genomewide Epistasis Analysis on Bacteria

HMMER-based microcin search using full microcin sequences and double-glycine signal region.

string based approach to check for the instertion element in bacterial genomes

In this repository, we have compiled the WGS analysis schematics of the bacterial isolates obtained from poultry manure of layer and broiler poultry farms