phages

WtP: Phage identification via nextflow and docker or singularity

Phigaro is a scalable command-line tool for predicting phages and prophages

A curated list of phage related software and computational resources for phage scientists, bioinformaticians and enthusiasts.

Phage-Host Interaction Search Tool

tyPPing and other methods for detecting phage-plasmids

Investigating the gut virus communities associated with colon cancer.

Software to predict the occurence of programmed ribosomal frameshifting in bacterial, phage, and viral genomes

The art of decorating a phage genome by gluing feature cutouts into it.

A fast Rust reimplementation of PHANOTATE

Running phispy, but on the web

Phage RBP classifier

The PhageBox is a digital microfluidics device that integrates temperature and magnetic control modules at the hardware level. This repository contains the embedded software which contains a finite state machine for representing PCR and a graphical user interface for visual feedback and operation.

This is a metagenomics pipeline to detect phages and Auxiliary Metabolic Genes (AMGs) from specific virtual genomes of bacteria (MAGs) in the human microbiome.

Code and data used to perform the tAI analysis in deCarvalho et al. (2023)

Code and data for the analysis of TF-binding sites positional entropy in phage genomes, used in Mascolo et al. (2022)

Fast and accurate whole-genome clustering of (actino) bacteriophages

PhageFilter uses a Sequence Bloom Tree (SBT) to filter bacteriophage reads from metagenomic files.

Tool to find mge (phages, plasmids, and transposons) in cdiff. Scripts that allow Clostyper to be run in slurm.

Comparative viromics pipeline designed to profile gut viral communities in neurodysbiosis and control cohorts. Implements de novo MEGAHIT assembly, geNomad prediction, CheckV quality assessment, and Bowtie2 read recruitment to characterize gut bacteriophage signatures in humanized mouse models.

Generate report cards for Phage genomes