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
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.
amR package suite: 1) amRdata, 2) amRml, 3) amRshiny
Decision-support framework for adaptive early stopping in Oxford Nanopore genome polishing.
A Nextflow pipeline for bacterial genome assembly, annotation, and functional gene discovery developed as part of GT BIOL7210 Computational Genomics Course.
python PhyloGenomic, Core and Fingerprint analyses software
Comprehensive WGS variant analysis of Pseudomonas aeruginosa (SRR34663677) — includes quality control, alignment (BWA-MEM), variant calling (GATK), annotation (SnpEff), and AMR interpretation.
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)
D2AFRICA bioinformatics tutorial
This repository contains the R codes and analysis objects associated with the AC phyllosphere bacterial collection
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