PPR-Meta-ZhuLab

PPR-MetaA tool for identifying phages and plasmids from metagenomic fragments using deep learning

INTRODUCTION

PPR-Meta is designed to identify metagenomic sequences as phages, chromosomes or plasmids. The program calculate three score reflecting the likelihood of each input fragment as phage, chromosome or plasmid. PPR-Meta can run either on the virtual machine or physical host. For non-computer professionals, we recommend running the virtual machine version of PPR-Meta on local PC. In this way, users do not need to install any dependency package. If GPU is available, you can also choose to run the physical host version. This version can automatically speed up with GPU and is more suitable to handle large scale data.

Please direct your questions or comments to fangzc@pku.edu.cn or hqzhu@pku.edu.cn

DOWNLOAD

Click "Manual-v1.1.pdf" to download the manual of PPR-Meta.
To run PPR-Meta on virtual machine, click "VM_Bioinfo.vdi.7z" (~3.0 GB) to download the virtual machine file. You can also click "Video_Guide.mp4" to download the short video guide to see how to use the virtual machine.
To run PPR-Meta on physical host, click "PPR-Meta_v1.1" to download the package.
The program is also available at https://github.com/zhenchengfang/PPR-Meta

DATA

All data used to train and test PPR-Meta, related results and scripts are stored here

CITATION

Fang, Z., Tan, J., Wu, S., Li, M., Xu, C., Xie, Z., & Zhu, H. (2019). PPR-Meta: a tool for identifying phages and plasmids from metagenomic fragments using deep learning. GigaScience, 8(6), giz066.

REFERENCES

Casjens S. (2003) Prophages and bacterial genomics: what have we learned so far?. Mol. Microbiol., 49, 277-300.
Frost,L.S. et al. (2005) Mobile genetic elements: the agents of open source evolution. Nat. Rev. Microbiol., 3, 722-732.
Krawczyk,P.S. et al. (2018) PlasFlow: predicting plasmid sequences in metagenomic data using genome signatures. Nucleic Acids Res..
Ren,J. et al. (2017) VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data. Microbiome, 5, 69.
Richter,D.C. et al. (2008) MetaSim: a sequencing simulator for genomics and metagenomics. PLoS ONE, 3, e3373.
Roux,S. et al. (2015) VirSorter: mining viral signal from microbial genomic data. PeerJ, 3, e985.
Sobecky,P.A. and Hazen,T.H. (2009) Horizontal gene transfer and mobile genetic elements in marine systems. Methods Mol. Biol., 532, 435-453.
Zhou,F. and Xu,Y. (2010) cBar: a computer program to distinguish plasmid-derived from chromosome-derived sequence fragments in metagenomics data. Bioinformatics, 26, 2051-2052.

Department of Biomedical Engineering and Center for Quantitative Biology, PKU