A tool for identifying phages and plasmids from metagenomic fragments using deep learning
☆44Apr 13, 2021Updated 4 years ago
Alternatives and similar repositories for PPR-Meta
Users that are interested in PPR-Meta are comparing it to the libraries listed below
Sorting:
- 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
- Predict prokaryotic host for phage metagenomic sequences☆55Sep 17, 2024Updated last year
- ☆18Apr 6, 2022Updated 3 years ago
- Identifying viruses from metagenomic data by deep learning☆150Jun 1, 2025Updated 9 months ago
- A tool for distinguish temperate phage-derived and virulent phage-derived sequence in metavirome data using deep learning☆26Nov 20, 2023Updated 2 years ago
- Source code of the VirSorter tool, also available as an App on CyVerse/iVirus (https://de.iplantcollaborative.org/de/)☆101Oct 3, 2020Updated 5 years ago
- VirHostMatcher: matching hosts of viruses based on oligonucleotide frequency (ONF) comparison☆31Jul 28, 2018Updated 7 years ago
- ☆33Jul 14, 2021Updated 4 years ago
- Workflow to assign Taxonomy to a bacteriophage genome isolate☆38Mar 25, 2025Updated 11 months ago
- WtP: Phage identification via nextflow and docker or singularity☆104Updated this week
- Accurate identification of bacteriophages from metagenomic data using Transformer☆22Nov 6, 2024Updated last year
- Ley Lab MetaGenome Profiler DataBase generator☆49Nov 9, 2022Updated 3 years ago
- ☆16Mar 11, 2024Updated last year
- Identify phage regions in bacterial genomes for masking purposes☆33Sep 5, 2019Updated 6 years ago
- ☆35Dec 20, 2023Updated 2 years ago
- A python library for predicting phage lifestyle based on genome sequence☆41Aug 9, 2023Updated 2 years ago
- Cenote-Taker2: Discover and Annotate Divergent Viral Contigs (Please use Cenote-Taker 3 instead)☆55Jan 19, 2024Updated 2 years ago
- Downstream processing of VAMB binning for Viral Elucidation☆54Jul 3, 2024Updated last year
- customizable pipeline to identify viral sequences from (meta)genomic data☆281Nov 28, 2024Updated last year
- Virus Identification By iteRative ANnoTation☆186Apr 15, 2024Updated last year
- GCN classifier for phage taxanomy classification☆31Nov 6, 2024Updated last year
- MARVEL: Metagenomic Analyses and Retrieval of Viral ELements☆51Apr 19, 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
- Fast and sensitive discovery of complete phages and prophages in bacterial genome sequences☆22Dec 16, 2024Updated last year
- ☆35Jun 26, 2025Updated 8 months ago
- SpacePHARER CRISPR Spacer Phage-Host pAiRs findER☆44May 8, 2024Updated last year
- Scripts to build high-quality genome-scale metabolic model by using a deep neural network to guide gapfilling☆18Mar 18, 2025Updated 11 months ago
- HOTSPOT is a hierarchical host prediction tool for plasmid contigs using Transformer.☆10Apr 22, 2024Updated last year
- Mining CRISPRs in Environmental Datasets☆119Feb 10, 2023Updated 3 years ago
- Software for prediction of plasmid sequences in metagenomic assemblies☆109Jun 28, 2021Updated 4 years ago
- An open database of vertebrate-virus interactions☆40Dec 16, 2025Updated 2 months ago
- ☆38Dec 6, 2023Updated 2 years ago
- Rapid discovery of novel prophages using biological feature engineering and machine learning☆37Dec 20, 2024Updated last year
- This is the codebase for Faucet, described in our manuscript: https://academic.oup.com/bioinformatics/article/34/1/147/4004871, by Roye R…☆18May 21, 2017Updated 8 years ago
- viralVerify: viral contig verification tool☆74Feb 19, 2026Updated last week
- AMR++ is a bioinformatic pipeline meant to aid in the analysis of raw sequencing reads to characterize the profile of antimicrobial resis…☆47Feb 16, 2026Updated 2 weeks ago
- geNomad: Identification of mobile genetic elements☆291Nov 10, 2025Updated 3 months ago
- Providing up-to-date phage genome databases, metrics and useful input files for a number of bioinformatic pipelines.☆78Apr 16, 2025Updated 10 months ago
- PHANOTATE: a gene caller for phages.☆84Dec 2, 2024Updated last year