AMR/VF LGT focused bacterial genomics analysis workflow

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

Detect complete horizontal gene transfer (HGT) event rapidly and accurately from complex metagenomics data.

A tool to detect acquired AMR genes directly from long read sequencing data.

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

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

A high-performance data pipeline built with Python and DuckDB for processing and analyzing Human Microbiome Project (HMP) bacterial genome data. Features include automated GenBank file processing, Prefect workflow orchestration, an interactive Streamlit dashboard for data exploration, and comprehensive test coverage. Perfect for bio researchers.

Food wastE biopEptiDe claSsifier: from microbial genome to biopeptides function

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

Bacterial plasmid annotation pipeline

Medium scale identification of genomic neighbors in bacterial genomes

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

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

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

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.

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

domain analyzer for analyzing interpro domains