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awesome-phages

A curated list of phage related software and computational resources for phage scientists, bioinformaticians and enthusiasts.
https://github.com/voorloopnul/awesome-phages

Last synced: 5 days ago
JSON representation

  • Annotation

    • Host prediction

      • iphop - **iPHoP** stands for **i**ntegrated **P**hage **H**ost **P**rediction. It is an automated command-line pipeline for predicting host genus of novel bacteriophages and archaeoviruses based on their genome sequences.
      • phirbo - A tool to predict prokaryotic hosts for phage (meta)genomic

    • Gene prediction-annotation

      • [web
      • multiPhATE2 - MultiPhATE is a command-line program that runs gene
      • Phanns - PhANNs is a tool to classify any phage ORF as one of 10
      • PHANOTATE - PHANOTATE is a tool to annotate phage genomes. It uses the
      • pharokka
      • Prokka - Prokka is not phage specific but is often used to annotate phages.

    • Genome prediction

      • Seeker - Seeker is a python library for discriminating between bacterial and
      • VIRify - VIRify: detection of phages and eukaryotic
      • [web

    • Prophage prediction

      • DEPhT - A new tool for identifying prophages in bacteria scanning hundreds to thousands of genomes and accurately extract complete (likely active) prophages from them. [Publicaiton](https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac273/6572362)
      • DBSCAN-SWA - An integrated tool for rapid prophage detection
      • hafeZ - A tool for identifying inducible prophage elements through read
      • Phigaro - Phigaro is a standalone command-line application that is able
      • PhageBoost - Rapid discovery of novel prophages using biological feature
      • PhiSpy - PhiSpy identifies prophages in Bacterial genomes. Given an
      • Vibrant - VIBRANT is a tool for automated recovery and annotation
      • VirSorter2 - VirSorter2 applies a multi-classifier, expert-guided
      • WTP - What the Phage is a scalable workflow that combines multiple prophage prediction programs, including several of the aforementioned. It starts out of the raw fasta or fastq files and generates an integrated summary of the results obtained from each of the selected tools.

  • Web tools

    • Gene prediction-annotation

      • Phamerator - Comparative genomics and genome exploration tool for bacteriophages.
      • Phaster - Rapid identification and annotation of prophage sequences within bacterial
      • Prophage Hunter - Prophage Hunter is a web server tool that employs several criteria to score how likely a prophage is beeing active within a bacterial genome. See also the paper [here](https://academic.oup.com/nar/article/47/W1/W74/5494712).
      • RAST - RAST (Rapid Annotation using Subsystem Technology) is a fully-automated service
      • [source

  • Miscellaneous

    • Gene prediction-annotation

      • bacteriophage.news - Bacteriophage.news is a virtual space that provides
      • millardlab - Lab from the University of Leicester focused on bacteriophages with plenty
      • phage.directory - Phage Directory curates a database of phage labs, phages, and host
      • phagesdb - The Actinobacteriophage database, more commonly known as PhagesDB, is a
      • phage.ai - PhageAI is an AI-driven software platform using advanced Machine Learning and
      • seaphages - SEA-PHAGES is a two-semester, discovery-based undergraduate research course
      • inphared - Providing up-to-date phage genome databases, metrics and
      • PHAGES2050 - a comprehensive AI-based Framework for Phage Research & Therapy

  • Kwnologe base

Programming Languages
Python 12 Perl 2 Jupyter Notebook 2 HTML 2 JavaScript 1 Nextflow 1
Categories
Annotation 20 Miscellaneous 8 Web tools 5 Kwnologe base 2
Sub Categories
Gene prediction-annotation 21 Prophage prediction 9 Genome prediction 3 Host prediction 2
Keywords
bioinformatics 3 nextflow 2 phages 2 phage 2 genomics 2 cwl 1 pipeline 1 viruses 1 workflow 1 bioinformatics-analysis 1 bioinformatics-pipeline 1 bioinformatics-tool 1 biological-data-analysis 1 genomic-data-analysis 1 genomic-regions 1 prophage 1 nextflow-pipelines 1 phage-identification 1 phage-sequences 1 annotate-phage-genomes 1 annotation 1 bacterial-genomes 1 functional-assignment 1 gene-finding 1 genome-annotation 1