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
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
Ultra-fast SNP/indel-level distance calculator for core genome MLST analysis in bacterial genomics
Exploring the diversity of CRISPR spacers in Campylobacter jejuni & coli
Machine learning-based secretion system annotation tool
Uncovering IS-mediated discord in bacterial genomes
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.
Comprehensive WGS variant analysis of Pseudomonas aeruginosa (SRR34663677) — includes quality control, alignment (BWA-MEM), variant calling (GATK), annotation (SnpEff), and AMR interpretation.
This repository contains the R codes and analysis objects associated with the AC phyllosphere bacterial collection
Pan-genomics of C difficile with linked reads
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.
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.
D2AFRICA bioinformatics tutorial
A Nextflow pipeline for bacterial and viral pathogen analysis — designed for public health applications.
Nextflow pipeline for comprehensive bacterial genome analysis from Illumina paired-end reads (QC, Assembly, AMR, Phylogeny, Virulence)
Pipeline para montagem direcionada (gene-a-gene) a partir de leituras pareadas.
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