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.
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
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 the following manuscript: Pell, M.E. et al., bioRxiv, 2024-04-01.
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.
D2AFRICA bioinformatics tutorial
python PhyloGenomic, Core and Fingerprint analyses software
A Nextflow pipeline for bacterial genome assembly, annotation, and functional gene discovery developed as part of GT BIOL7210 Computational Genomics Course.
Zoonoticus is a comprehensive tool for predicting zoonotic potential, antimicrobial resistance risk, and virulence profiles of bacterial genomes. Powered by Zento, it helps researchers rapidly identify bacteria capable of crossing species barriers and posing public health threats.
Uncovering IS-mediated discord in bacterial genomes
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