bacteriophage

Local version of the virus identification and analysis web server (tool set)

Bacteriophage discovery & characterization pipeline (Nextflow DSL2) — FastQC, Kraken2, SPAdes, VirSorter2, CheckV, BACPHLIP, Phrokka, Prokka, vContact2, vHULK, BLAST

TrIdent- Transduction Identification: Automatic detection, classification and characterization of active transduction events in microbiomes.

LLM-powered classification of phage protein functions to identify strong lytic candidates against Klebsiella, using transfer learning and biological embeddings.

Shiny apps in R for plotting lysis curves & reformatting FASTA files

SaPhARI: An Adaptable Bioinformatics Tool for the Discovery of Novel Phage Satellites

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.

Detect elevations and gaps in read coverage on metagenome contigs or assembled genomes

R Shiny app for publication-ready CFU plotting, statistics, and reproducible figure exports

Desktop FASTQ QC and trimming without terminal fear

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.

Plotting lysis curves

📑Reports and bioinformatics analyses from internship in Indonesia

End-to-end profile-HMM protein family discovery app — Shiny for Python, built with ChatGPT. Covers alignment, HMM building, database search, hit classification, synteny, phylogeny, and reproducible export.

Free browser-based tool for designing 96-well plate dilution experiments

Prediction of bacterial host for phage

Plaque counts to PFU/mL - single-file calculator with replicates, stats, and Excel export

Creation of a local database for bacteriophages

Benchmarking universal, topology-specific, and context-aware signatures for bacteriophage holin prediction

Staphylococcus aureus bakteriyofaj izolatlarinin assembly ve karakterizasyon ciktilari (metaviralSPAdes, CheckV, BACPHLIP, vContact2)