Local version of the virus identification and analysis web server (tool set)
bioinformatics virus taxonomy lifestyle metagenomic-analysis host-prediction bacteriophage dna-virus
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May 13, 2026 - Python
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bacteriophage
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Bacteriophage discovery & characterization pipeline (Nextflow DSL2) — FastQC, Kraken2, SPAdes, VirSorter2, CheckV, BACPHLIP, Phrokka, Prokka, vContact2, vHULK, BLAST
nextflow bioinformatics-pipeline viral-metagenomics dsl2 bacteriophage virsorter2 checkv phage-genomics
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Aug 3, 2026 - Nextflow
TrIdent- Transduction Identification: Automatic detection, classification and characterization of active transduction events in microbiomes.
pattern-matching metagenomics horizontal-gene-transfer phage transduction sequencing-coverage bacteriophage transductomics virus-like-particle
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Sep 1, 2026 - R
LLM-powered classification of phage protein functions to identify strong lytic candidates against Klebsiella, using transfer learning and biological embeddings.
hackathon transfer-learning phage antimicrobial-resistance protein-classification klebsiella protein-embeddings bacteriophage esm-model phagos
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May 22, 2025 - Jupyter Notebook
SaPhARI: An Adaptable Bioinformatics Tool for the Discovery of Novel Phage Satellites
bioinformatics genomics computational-biology metagenomics bioinformatics-pipeline microbial-genomics microbiology comparative-genomics genome-mining phage sequence-analysis bacteriophage satellite-phages
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Apr 27, 2026 - Python
Cocktail is a program for mathematical modelling of bacteriophage (phage) infection kinetics. Cocktail is a Windows 64-bit program and the source code can be developed in the directions that users see fit. This will be updated soon with a link to the scientific publication describing the program.
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Nov 14, 2022
Detect elevations and gaps in read coverage on metagenome contigs or assembled genomes
pattern-matching metagenomics read-mapping transposable-elements structural-variants sequencing-coverage mobile-genetic-elements prophages bacteriophage
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Aug 8, 2025 - HTML
Computational analysis of bacteriophage genomes including genome feature extraction, metadata integration, QC filtering, and large-scale statistical analysis.
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Mar 5, 2026 - Python
Staphylococcus aureus bakteriyofaj izolatlarinin assembly ve karakterizasyon ciktilari (metaviralSPAdes, CheckV, BACPHLIP, vContact2)
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Aug 3, 2026 - Python
Prediction of bacterial host for phage
python host crispr phage bacterium bacteriophage identification-of-hosts predicting-virus-host-pairs
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Jun 2, 2022 - C++
A multi-modal 3D voxel tracking, co-registration, and parallel spatial filtering pipeline designed to analyze and validate the biophysical, morphological, and pathognomonic convergence between historical 2D phage virus silhouettes and modern 3D cebidiomorphic Pycnogonida parasitic vectors.
medical-imaging finite-differences biophysics pycuda voxel-grid anisotropic-diffusion cuda-kernel bacteriophages bacteriophage dicom-processing pycnogonida oncology-tracking pathology-automation scipy-spatial multi-modal-registration cancer-moonshot tritium-effusion radiotoxic-kinetics
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Jul 6, 2026 - Python
📑Reports and bioinformatics analyses from internship in Indonesia
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Sep 1, 2024 - HTML
A Nextflow pipeline for the detection, quality assessment, annotation, and classification of bacteriophages from metagenomically assembled contigs
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Jun 8, 2026 - Nextflow
Predicting bacteria-phage interactions given phage and target bacterias sequenced genomes as well as hostrange interaction information. MSc Thesis @ DTU Healthtech
random-forest feedforward-neural-network bacteria phylogeny mlp-classifier bacterial-genomes downsampling bacteriophage minhashing bacteriophage-genomes
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Jun 17, 2026 - Jupyter Notebook
Creation of a local database for bacteriophages
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Sep 26, 2024 - R
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
Python code for implementing antiviral mass-balance in pre-harvest herbal plants.
python environmental-engineering wastewater mass-balance plant-viruses rt-pcr bacteriophage antiviral phytoremediation plaque-assay
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Jul 1, 2026 - Python
End-to-end bacteriophage genome characterisation and phage-therapy screening — a one-click macOS app.
macos bioinformatics genomics computational-biology genome-annotation phage bacteriophage phage-therapy phage-genomics
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Jul 22, 2026 - Python
Langevin dynamics simulation of bacteriophage-bacteria interaction
virus physics physics-simulation biophysics langevin-dynamics brownian-motion condensed-matter-physics bacteriophage self-propelled-particles
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Oct 7, 2023 - Python
Bakteriyofaj genom gorsellestirmesi icin R/Python kodlari (Bakta GFF3'ten dairesel genom haritasi)
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Aug 3, 2026 - R
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