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
A transparent ONT bacterial assembly case study for an *Acinetobacter* barcode07 isolate, built not only to generate an assembly, but to show how raw reads become an interpretable genome through QC evidence, assembler comparison, graph checks, phylogeny, annotation, documented decisions, and honest limitations.
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
Pan-genomics of C difficile with linked-read technollgy
Automated bacterial genomic analysis · AI-assisted clinical interpretation · PCR primer design (research use only)
Comprehensive WGS variant analysis of Pseudomonas aeruginosa (SRR34663677) — includes quality control, alignment (BWA-MEM), variant calling (GATK), annotation (SnpEff), and AMR interpretation.
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.
🧬🍏✨ 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.
A Nextflow pipeline for bacterial and viral pathogen analysis — designed for public health applications.
Decision-support framework for adaptive early stopping in Oxford Nanopore genome polishing.
A modular, reproducible, and automated Bash pipeline for bacterial isolate whole-genome sequencing analysis from Illumina paired-end reads, including quality control, taxonomic classification, genome assembly, genome characterization, and coverage estimation.
A Nextflow pipeline for bacterial genome assembly, annotation, and functional gene discovery developed as part of GT BIOL7210 Computational Genomics Course.
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