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

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

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

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

Comprehensive WGS variant analysis of Pseudomonas aeruginosa (SRR34663677) — includes quality control, alignment (BWA-MEM), variant calling (GATK), annotation (SnpEff), and AMR interpretation.

Pan-genomics of C difficile with linked-read technollgy

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

De novo genome assembly and structural annotation of bacterial isolate SRR25083113 using SPAdes, Prodigal, Barrnap, and ARAGORN — a macOS ARM–compatible pipeline alternative to QUAST/Prokka.

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.

A Nextflow pipeline for bacterial and viral pathogen analysis — designed for public health applications.

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

D2AFRICA bioinformatics tutorial

A Nextflow pipeline for bacterial genome assembly, annotation, and functional gene discovery developed as part of GT BIOL7210 Computational Genomics Course.