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

Phage-focused genome annotation and comparative genomics workflow integrating structural gene prediction, evidence-supported functional annotation, and INPHARED nearest-phage analysis.

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.

A comprehensive pan-immunophagomic analysis of Pseudomonas aeruginosa, characterizing CRISPR-Cas arrays, prophage integrations, and innate bacterial defense repertoires across diverse clinical isolates.

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

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

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.

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

Desktop FASTQ QC and trimming without terminal fear

Plotting lysis curves

Prediction of bacterial host for phage

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

📑Reports and bioinformatics analyses from internship in Indonesia

Python tools that sped up bacteriophage genome annotation at the Eliava Institute: GeneMark gene calls to FASTA, NCBI BLAST, PHROGs and HHpred hit mapping, EMBL export.