💾 📃 "Reads to report" for public health and clinical microbiology
public-health report variant-calling bacteria fastq phylogenomics denovo-assembly genotyping resistome virulome
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Dec 9, 2025 - Perl
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resistome
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A resistome profiler for Graphing Resistance Out Of meTagenomes
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May 11, 2020 - Go
JAMIRA is a reproducible Workflow for Integrative Exploration of Genomic Features of prokariotes
snakemake comparative-genomics genomic-data-analysis genomic-islands resistome virulence-genes bioinformatics-workflow prophages
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Nov 10, 2020 - Python
A pipeline for Detecting Resistome Associated taXa
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Jun 11, 2018 - Groovy
This tool provides a modular WDL-Docker-Cromwell environment for rMAP, a bioinformatics pipeline for analyzing microbial genomic data, genome assembly & profiling of the resistome, mobilome & virulome, as well as pangenome & MLST typing, BLASTn & phylogenetic analysis. It includes all required tools, enabling reproducible & scalable analysis
docker microbial-genomics variant-calling cromwell modular-design wdl-workflow plasmids phylogenetic-analysis resistome virulome rmap mobilome pangenome-analysis mlst-typing eskapee
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Jun 3, 2026 - WDL
Mapping, snps calling, phylogeny
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Oct 2, 2019 - Shell
Bacterial analysis toolbox for full ESKAPEE pathogen characterisation and profiling the resistome, mobilome, virulome & phylogenomics using WGS
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Sep 28, 2020 - Shell
A WDL-based workflow for profiling Klebsiella & E. coli genomes using Kleborate. Supports local execution with Cromwell both local & cloud deployment in Terra, enabling automated analysis of assemblies with docker & integration with Terra data tables for scalable genomic surveillance.
microbial-genomics cromwell escherichia-coli resistome virulome genomic-surveillance kleborate klebsiella-species wdl-based-workflow
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Aug 10, 2025 - Shell
Predicts bacterial resistome
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Jun 11, 2019 - R
A Computational Pipeline for Ranking Resistome Risk of Metagenomic Samples
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Jan 26, 2026 - Python
Zero-shot protein language model pipeline for mutational tolerance scoring of antibiotic resistance genes in ESKAPE pathogens
deep-mutational-scanning resistome antimicrobial-resistance antibiotic-resistance-genes zero-shot-prediction protein-language-models esm2 eskape-pathogens mutational-tolerance bacterial-evolution
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Apr 24, 2026
A comprehensive pan-immunophagomic analysis of Pseudomonas aeruginosa, characterizing CRISPR-Cas arrays, prophage integrations, and innate bacterial defense repertoires across diverse clinical isolates.
bioinformatics comparative-genomics virology pathogen-genomics resistome prophage pseudomonas-aeruginosa crispr-cas phage-defense bacteriophage pan-genomics viral-host-interaction immunophagomics
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Aug 4, 2026 - Python
A modular and reproducible metagenomic workflow for integrated antimicrobial resistance, taxonomic and plasmid characterization.
bioinformatics args metagenomics amr plasmid resistome antimicrobial-resistance-genes antimicrobial-resistance taxonomic-profiling one-health pathogen-surveillance
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Aug 28, 2026 - R
Graph-based pangenomic and synteny analysis of Helicobacter pylori (n=41 complete RefSeq genomes) using PPanGGOLiN, with reproducible workflows for annotation (Prokka), ANI quality control (FastANI), core-genome phylogeny (MAFFT + IQ-TREE 2), resistome profiling (AMRFinderPlus), and publication-grade visualizations.
bioinformatics microbial-genomics comparative-genomics synteny phylogenomics pangenomics mafft resistome prokka fastani bacterial-genomics amrfinderplus iqtree2 helicobacter-pylori ppanggolin
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Aug 4, 2026 - Python
Oral metagenomic analysis of antimicrobial resistance genes associated with periodontitis
bioinformatics metagenomics microbiome resistome antimicrobial-resistance rstars oral-microbiome periodontitis
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May 13, 2026 - R
A number of pipelines that are managed by Gnu Make for conducting various analyses on high-throughput NGS
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Aug 12, 2020 - Shell
A WGCNA pipeline systematically interrogating the Campylobacter resistome through topological network scaling to uncover co-expressed stress-response loci and significant module-trait biological correlations.
network-topology reproducible-research systems-biology computational-biology bioinformatics-pipeline amr transcriptomics r-stats wgcna bacteriology resistome antimicrobial-resistance stress-response campylobacter host-pathogen-interactions co-expression-network scale-free-network module-eigengene
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Apr 21, 2026 - R
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