Machine learning-based secretion system annotation tool
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Mar 18, 2026 - Python
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bacterial-genomics
Here are 15 public repositories matching this topic...
Exploring the diversity of CRISPR spacers in Campylobacter jejuni & coli
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Jul 24, 2026 - Python
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
bioinformatics supermatrix phylogenetics comparative-genomics comparative-genomics-studies phylogeny whole-genome-sequencing whole-genome evolutionary-biology concatination bacterial-genomics
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Sep 5, 2025 - Python
Automated bacterial genomic analysis · AI clinical interpretation · PCR primer design
bioinformatics ai genomics mlst antimicrobial-resistance fastapi bacterial-genomics pcr-primer-design clinical-microbiology
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May 6, 2026 - Python
Pan-genomics of C difficile with linked-read technollgy
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Jul 29, 2025 - Python
🧬🍏✨ Graph-aware contextual annotation of targeted genomic features.
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Apr 24, 2026 - Python
Decision-support framework for adaptive early stopping in Oxford Nanopore genome polishing.
docker machine-learning bioinformatics decision-support oxford-nanopore genome-assembly fastapi oxford-nanopore-sequencing bacterial-genomics genome-polishing
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Jul 31, 2026 - Python
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)
python bioinformatics genomics data-visualization scientific-computing eggnog-mapper genome-visualization bacterial-genomics circular-genome-map cog-categories
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Feb 10, 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
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May 27, 2026 - Python
python PhyloGenomic, Core and Fingerprint analyses software
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Jun 12, 2026 - Python
reproducible Snakemake pipeline for bacterial hybrid assembly.
python snakemake nanopore illumina genome-assembly masurca snakemake-workflow hybrid-assembly quast polca snakemake-pipeline flye bacterial-genomics filtlong
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Jun 30, 2026 - Python
Reusable comparative bacterial genomics pipeline for assembled bacterial genome FASTA files using QUAST, Bakta, FastANI, Panaroo, and FastTree.
bioinformatics comparative-genomics phylogeny quast fastani panaroo bacterial-genomics bakta genomics-pipeline
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May 27, 2026 - Python
Pipeline para montagem direcionada (gene-a-gene) a partir de leituras pareadas.
python-script bioinformatics-pipeline viral-genomics ngs-analysis laboratory-reports arboviruses genomics-analysis public-health-surveillance bacterial-genomics genome-assembly-utilities
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Aug 6, 2025 - Python
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.
machine-learning bioinformatics-pipeline microbiology disease-surveillance infectious-diseases antimicrobial-resistance bacterial-genomics zoonotic-diseases pathogen-prediction bacterial-virulence
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Dec 30, 2025 - Python
Bioinformatics workflows, Python scripts, and R templates developed during the adaptive laboratory evolution of Rhodococcus ruber under high pyrene concentrations. Includes genome assembly, polishing, comparative genomics, mutation analysis, and visualization tools.
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Jun 12, 2026 - Python
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