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

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

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

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

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

domain analyzer for analyzing interpro domains

metegnome sequence extractions from MAGs

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

Script to design core genome phylogeny using bacterial genome assemblies

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

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

Medium scale identification of genomic neighbors in bacterial genomes

Bacterial plasmid annotation pipeline

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

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

WGS- Metasociomic- analysing bacterial social interactions in metagenomes of longitudinally collected samples of human microbiomes