Bacterial surveillance pipeline.

pathogen agnostic general workflow for genome assembly of Illumina paired-end sequence data

Automatically and reproducibly runs Autocycler (v. 0.4.0) with additional long-read QC, assembly reorientation, and optional short-read QC and polishing.

general workflow for genome assembly-based SNP phylogeny with optional recombination masking

Ultra-fast SNP/indel-level distance calculator for core genome MLST analysis in bacterial genomics

Machine learning-based secretion system annotation tool

Exploring the diversity of CRISPR spacers in Campylobacter jejuni & coli

This repository provides an easy-to-use Python-based pipeline for reconstructing phylogenetic trees from whole bacterial genomes. It automates the process of identifying orthologous single-copy genes, aligning sequences, trimming alignments, and generating a concatenated supermatrix ready for phylogenetic analysis. The pipeline requires only .fasta

amR package suite: 1) amRdata, 2) amRml, 3) amRshiny

Automated Software Catalog Creator for Bacterial Data Analysis

Automated bacterial genomic analysis · AI clinical interpretation · PCR primer design

🧬🍏✨ Graph-aware contextual annotation of targeted genomic features.

This repository contains scripts used to collect and analyze data from whole genome sequences of clinical Streptococcus agalactiae (Group B Strep) isolates for the project described in Pell et al., mBio, 2026.

Decision-support framework for adaptive early stopping in Oxford Nanopore genome polishing.

Curated genomic database of Staphylococcal Pathogenicity Islands (SaPIs), mobile genetic elements in Staphylococcus aureus that contribute to virulence through carriage of enterotoxin and other virulence-associated genes.

D2AFRICA bioinformatics tutorial

A genomic toolkit for sliding-window GC content/skew circular mapping, XLSX-to-FASTA protein extraction, and EggNOG-mapper results parsing for functional category distribution. Provides automated, high-resolution visualization for bacterial genomes. Post-analysis for Genomics NGS Analysis Team 新北市汐止區新台五路 (Taiwan © 2017-2018 Genomics)

nf-rMAP: Nextflow-powered microbial genomics pipeline for rapid antimicrobial resistance analysis. Implements rMAP's core functionality with cloud-native scalability, enhanced QC, & modular workflows. Processes Illumina data through assembly, annotation, AMR detection & phylogenetics.

This repository contains the R codes and analysis objects associated with the AC phyllosphere bacterial collection

python PhyloGenomic, Core and Fingerprint analyses software