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https://github.com/voorloopnul/awesome-phages

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

List: awesome-phages

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

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README 

        
# Awesome phages



A curated list of awesome phage related software and other resources to facilitate the life of phage scientists,

bioinformaticians and enthusiasts.



## How to contribute



If you want to add a link, please try to follow these soft rules:



- Position your resource in alphabetical order.

- Add section if needed.

- Add section title to Table of contents.

- Search previous suggestions before making a new one, as yours may be a duplicate.

- Add your links using another entry as inspiration

- Check your spelling and grammar.

- Make sure your text editor is set to remove trailing whitespace.

- Send a Pull Request.

- Add short description in your Pull Request of why the project/resource/tool is awesome.



## Table of Contents



- [Annotation](#annotation)

  - [Genome prediction](#genome-prediction) 

  - [Host prediction](#host-prediction)

  - [Prophage prediction](#prophage-prediction)

  - [Gene prediction annotation](#gene-prediction-annotation)

- [Web tools](#web-tools)

- [Miscellaneous](#miscellaneous)



## Annotation



### Genome prediction



- **[Seeker](https://github.com/gussow/seeker)** - Seeker is a python library for discriminating between bacterial and

phage genomes. Seeker is based on an LSTM deep-learning models and does not rely on a reference genome, genomic

alignment or any direct genome comparison.

[ [web](http://seeker.pythonanywhere.com/predict/) ]

- **[VIRify](https://github.com/EBI-Metagenomics/emg-viral-pipeline)** - VIRify: detection of phages and eukaryotic

viruses from metagenomic and metatranscriptomic assemblies.



### Host prediction



- **[iphop](https://bitbucket.org/srouxjgi/iphop/src/main/)** - **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](https://github.com/aziele/phirbo)** - A tool to predict prokaryotic hosts for phage (meta)genomic

sequences. The tool uses information on sequence similarity between phage and bacteria genomes as well as sequence

relatedness among bacteria.



### Prophage prediction



- **[DEPhT](https://github.com/chg60/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](https://github.com/HIT-ImmunologyLab/DBSCAN-SWA)** - An integrated tool for rapid prophage detection

and annotation.

- **[hafeZ](https://github.com/Chrisjrt/hafeZ)** - A tool for identifying inducible prophage elements through read

mapping.

- **[Phigaro](https://github.com/bobeobibo/phigaro)** - Phigaro is a standalone command-line application that is able

to detect prophage regions taking raw genome and metagenome assemblies as an input.

- **[PhageBoost](https://github.com/ku-cbd/PhageBoost)** - Rapid discovery of novel prophages using biological feature

engineering and machine learning.

- **[PhiSpy](https://github.com/linsalrob/phispy)** - PhiSpy identifies prophages in Bacterial genomes. Given an

annotated genome it will use several approaches to identify the most likely prophage regions.

- **[Vibrant](https://github.com/AnantharamanLab/VIBRANT)** - VIBRANT is a tool for automated recovery and annotation

of bacterial and archaeal viruses, determination of genome completeness, and characterization of viral community

function from metagenomic assemblies.

- **[VirSorter2](https://github.com/jiarong/VirSorter2)** - VirSorter2 applies a multi-classifier, expert-guided

approach to detect diverse DNA and RNA virus genomes.

- **[WTP](https://github.com/replikation/What_the_Phage)** - 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.



### Gene prediction-annotation



- **[multiPhATE2](https://github.com/carolzhou/multiPhATE2)** - MultiPhATE is a command-line program that runs gene

finding and the PhATE annotation code over user-specified phage genomes, then performs gene-by-gene comparisons among

the genomes.

- **[Phanns](https://github.com/Adrian-Cantu/PhANNs)** - PhANNs is a tool to classify any phage ORF as one of 10

structural protein class, or as "others". It uses an ensemble of Artificial Neural Networks. [[web](https://edwards.sdsu.edu/phanns)]

- **[PHANOTATE](https://github.com/deprekate/PHANOTATE)** - PHANOTATE is a tool to annotate phage genomes. It uses the

assumption that non-coding bases in a phage genome is disadvantageous, and then populates a weighted graph to find the

optimal path through the six frames of the DNA where open reading frames are beneficial paths, while gaps and overlaps

are penalized paths.

- **[pharokka](https://github.com/gbouras13/pharokka)** Pharokka is a rapid standardised annotation program for bacteriophages. It is inspired on [Prokka](https://github.com/tseemann/prokka). Gene prediction is performed with  **[PHANOTATE](https://github.com/deprekate/PHANOTATE) and functional annotation is based on the [PHROGs database](https://phrogs.lmge.uca.fr)



- **[Prokka](https://github.com/tseemann/prokka)** - Prokka is not phage specific but is often used to annotate phages.



## Web tools



- **[Patric](https://www.patricbrc.org/)** PATRIC, the Pathosystems Resource Integration Center, provides integrated

data and analysis tools to support biomedical research on bacterial infectious diseases.

- **[Phamerator](https://phamerator.org/)** - Comparative genomics and genome exploration tool for bacteriophages.

[ [source](https://github.com/scresawn/phamerator) ]

- **[Phaster](https://phaster.ca/)** - Rapid identification and annotation of prophage sequences within bacterial

genomes and plasmids.

- **[Prophage Hunter](https://pro-hunter.genomics.cn/index.php/Home)** - 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](https://rast.nmpdr.org/)** - RAST (Rapid Annotation using Subsystem Technology) is a fully-automated service

for annotating complete or nearly complete bacterial and archaeal genomes. It provides high quality genome annotations

for these genomes across the whole phylogenetic tree.



##  Miscellaneous



- **[bacteriophage.news](https://www.bacteriophage.news/)** - Bacteriophage.news is a virtual space that provides

general news, research articles & patient stories on phage therapy.

- **[inphared](https://github.com/RyanCook94/inphared)** - Providing up-to-date phage genome databases, metrics and

useful input files for a number of bioinformatic pipelines.

- **[millardlab](http://millardlab.org/)** - Lab from the University of Leicester focused on bacteriophages with plenty

of resources for phage bioinformatics.

- **[phage.directory](https://phage.directory/)** - Phage Directory curates a database of phage labs, phages, and host

strains to advance research and phage therapy.

- **[phagesdb](https://phagesdb.org/)** - The Actinobacteriophage database, more commonly known as PhagesDB, is a

database-backed website that gathers and shares information related to the discovery, characterization and genomics of

viruses that prefer to infect Actinobacterial hosts

- **[PHAGES2050](https://github.com/ptynecki/PHAGES2050)** - a comprehensive AI-based Framework for Phage Research & Therapy

- **[phage.ai](https://phage.ai/)** - PhageAI is an AI-driven software platform using advanced Machine Learning and

Natural Language Processing techniques for deeper understanding of the bacteriophages genomics.

- **[seaphages](https://seaphages.org/)** - SEA-PHAGES is a two-semester, discovery-based undergraduate research course

that begins with simple digging in the soil to find new viruses, but progresses through a variety of microbiology

techniques and eventually to complex genome annotation and bioinformatic analyses.



## Kwnologe base



- **[Viral taxonomy](https://talk.ictvonline.org/ictv-reports/ictv_online_report/)**