Python script to extract and visualize AMR data from AMRFinderPlus outputs, generating detailed reports and binary heatmaps
-
Updated
Oct 23, 2024 - Python
#
amrfinderplus
Here are 7 public repositories matching this topic...
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.
linux bash bioinformatics genomics amr microbiology mlst wgs spades samtools whole-genome-sequencing bowtie2 antimicrobial-resistance quast kraken2 bracken abricate checkm bacterial-genomics amrfinderplus
-
Updated
Aug 20, 2026 - Shell
Characterising the AMR landscape via EDA and predictive modelling, and developing an integrated pipeline that bridges genomic surveillance data to protein targets and ligand candidates for downstream drug discovery.
machine-learning bioinformatics-pipeline drug-discovery molecular-modeling antimicrobial-resistance xgboost-classifier amrfinderplus
-
Updated
Jun 2, 2026 - Jupyter Notebook
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
-
Updated
Aug 4, 2026 - Python
AI-assisted pipeline for mining candidate Staphylococcus invasome and virulence-associated genes from assembled genome FASTA files.
python bash bioinformatics pipeline genomics reproducible-research conda virulence abricate staphylococcus bacterial-genomics bakta amrfinderplus invasome vfdb
-
Updated
May 27, 2026 - Python
Genomic identification and characterization of antimicrobial resistance determinants in Klebsiella pneumoniae NTUH-K2044 using AMRFinderPlus and genome sequence analysis.
bioinformatics genomics amr microbial-genomics antimicrobial-resistance klebsiella-pneumoniae bacterial-genomics amrfinderplus
-
Updated
Aug 30, 2026 - Jupyter Notebook
AMR prediction pipeline for Acinetobacter baumannii using whole-genome sequencing and machine learning (Random Forest, Logistic Regression) with SHAP-based gene importance analysis.
machine-learning logistic-regression feature-engineering genome-analysis antibiotics random-forest-classifier bacterial-genomes antimicrobial-resistance shap genome-features amrfinderplus resistance-phenotype
-
Updated
May 22, 2026 - Jupyter Notebook
Add this topic to your repo
To associate your repository with the amrfinderplus topic, visit your repo's landing page and select "manage topics."