This repository contains scripts used in the manuscript "Massive expansion of human gut bacteriophage diversity"
☆20Feb 3, 2021Updated 5 years ago
Alternatives and similar repositories for GPD
Users that are interested in GPD are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Code for de novo discovery of viral families in virome data☆16Jun 20, 2024Updated 2 years ago
- Fast and sensitive discovery of complete phages and prophages in bacterial genome sequences☆23Dec 16, 2024Updated last year
- Prophage Activity Estimator☆33May 30, 2024Updated 2 years ago
- Downstream processing of VAMB binning for Viral Elucidation☆55Jul 3, 2024Updated last year
- ViromeScan allows the user to explore and taxonomically characterize the virome from metagenomic reads, efficiently denoising samples fro…☆13Feb 13, 2023Updated 3 years ago
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- Predict prokaryotic host for phage metagenomic sequences☆56Sep 17, 2024Updated last year
- Scripts to quality control for metagenomic raw data, including removing the adapters, low quality reads, bases or PCR duplicates☆18Aug 13, 2020Updated 5 years ago
- A containerized bioinformatics pipeline for viral metagenomic data analysis☆39Apr 9, 2026Updated 2 months ago
- ☆37Dec 6, 2023Updated 2 years ago
- Workflow to assign Taxonomy to a bacteriophage genome isolate☆41Apr 20, 2026Updated 2 months ago
- NCBI-style taxdump files for International Committee on Taxonomy of Viruses (ICTV)☆22May 3, 2025Updated last year
- detect temperate phage (active prophage) in assembled bacterial genome sequences☆15Feb 10, 2022Updated 4 years ago
- Workflow to rapidly quantify taxa from all domains of life, directly from short-read human gut metagenomes☆75Dec 1, 2025Updated 7 months ago
- NCBI taxonomic identifier (taxid) changelog, including taxids deletion, new adding, merge, reuse, and rank/name changes.☆28May 15, 2026Updated last month
- Serverless GPU API endpoints on Runpod - Get Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- Binning Virus Genomes from Metagenomes☆75Jul 13, 2022Updated 3 years ago
- WtP: Phage identification via nextflow and docker or singularity☆107Mar 19, 2026Updated 3 months ago
- This is graphanalyzer.py, a script designed to automatically interpret the outputs generated by vConTACT2 when using the INPHARED databas…☆19Nov 29, 2023Updated 2 years ago
- ☆22Sep 26, 2025Updated 9 months ago
- VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies☆152Updated this week
- A wrapper to identify, bin, classify, and predict host-viral relationship for viruses☆91Dec 27, 2024Updated last year
- A simple program to classify the lifestyle of phages.☆17May 22, 2023Updated 3 years ago
- 🫧🧬 From fragmented assemblies to high-quality bacteriophage genomes☆84Dec 4, 2025Updated 6 months ago
- Detection of NCLDV signatures in 'omic data☆35Dec 28, 2025Updated 6 months ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Phage annotations and predictions. A spae is a prediction or foretelling. We'll foretell you what your phage is doing!☆46Jun 1, 2026Updated last month
- Snakemake workflow to detect and classify viruses in metagenome assemblies.☆19Feb 14, 2024Updated 2 years ago
- Small pipeline to cluster viral genomes based on their k-mer content. WiP☆20May 28, 2026Updated last month
- PHANOTATE: a gene caller for phages.☆91Dec 2, 2024Updated last year
- ☆13Feb 29, 2024Updated 2 years ago
- A python library for predicting phage lifestyle based on genome sequence☆41Aug 9, 2023Updated 2 years ago
- SpacePHARER CRISPR Spacer Phage-Host pAiRs findER☆48May 8, 2024Updated 2 years ago
- Step-wise assembly of the neonatal virome modulated by breast feeding.☆11Aug 20, 2021Updated 4 years ago
- Precise phylogenetic analysis of microbial isolates and genomes from metagenomes☆168Jun 10, 2026Updated 3 weeks ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Systematic search of all known anti-phage systems.☆173May 5, 2026Updated last month
- Main development repository for SpreadGL☆22Jun 18, 2026Updated last week
- Iterative Gene clUster Analysis, a high-throughput method for gene cluster family identification.☆17Jun 4, 2026Updated 3 weeks ago
- Virus Identification By iteRative ANnoTation☆197Apr 15, 2024Updated 2 years ago
- A pipeline for lightweight screening of Eukaryotic genomes and transcriptomes for recent HGT☆14Aug 26, 2025Updated 10 months ago
- a pipeline to cluster proteins into families☆10Apr 1, 2020Updated 6 years ago
- Predict prokaryotic hosts for phage (meta) genomic sequences☆11Apr 4, 2022Updated 4 years ago