导读
学习宏病毒组。
| 分析工具 | 特点 | 发表杂志 | 发表时间 | 被引量 |
|---|---|---|---|---|
| VirSorter | 组装，PERL | PeerJ | 2015 | 363 |
| VirFinder | 组装，R k-mer | Microbiome | 2017 | 130 |
| GOTTCHA | reads, PERL | Nucleic Acids Res | 2015 | 104 |
| ViromeScan | reads, shell集成，真核 | BMC Genomics | 2016 | 65 |
| VIP | 组装，shell集成 | Scientific reports | 2016 | 57 |
| MARVEL | 组装, python, binning | Frontiers in Genetics | 2018 | 34 |
| Prophage Hunter | BGI网页工具 | Nucleic Acids Res | 2019 | 9 |
1. VirSorter
鉴别病毒序列
文章：VirSorter: mining viral signal from microbial genomic data
VirSorter Github: https://github.com/simroux/VirSorter
VirSorter2 Github: https://github.com/jiarong/VirSorter2
分析流程：
- 组装：MetaSPAdes
- 抽提病毒序列1：VirSorter (gene enrichment based method)
- 抽提病毒序列2：VirFinder (k-mer frequency based method)
- 病毒序列分类：NCBI viral RefSeq sequences, NCBI taxonomy data
- 基因预测：MetaProdigal
- crAss-like噬菌体检测
- Tentative病毒contig鉴定
- Pfam结构蛋白鉴定病毒
- 病毒组样品聚类
- 前噬菌体分析
参考：
Metagenome Data on Intestinal Phage-Bacteria Associations Aids the Development of Phage Therapy against Pathobionts.
Cell Host & Microbe. 2020
2. VirFinder
VirFinder: R package for identifying viral sequences from metagenomic data using sequence signatures。基于病毒序列 k -mers词频和机器学习识别病毒序列的方法。 此方法利用了常用的序列k -mers构建序列相量，构建机器学习分类器，不需要参考病毒序列数据库，显著提高了病毒序列识别的速度和准确性，将有助于在宏基因组学时代下对病毒的研究。
文章：VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data
VirFinder Github: https://github.com/jessieren/VirFinder
分析流程：
- 组装：MetaSPAdes
- 抽提病毒序列1：VirSorter (gene enrichment based method)
- 抽提病毒序列2：VirFinder (k-mer frequency based method)
- 病毒序列分类：NCBI viral RefSeq sequences, NCBI taxonomy data
- 基因预测：MetaProdigal
- crAss-like噬菌体检测
- Tentative病毒contig鉴定
- Pfam结构蛋白鉴定病毒
- 病毒组样品聚类
- 前噬菌体分析
工具比较：
参考：
1 Metagenome Data on Intestinal Phage-Bacteria Associations Aids the Development of Phage Therapy against Pathobionts.
Cell Host & Microbe. 2020
2 VirFinder：基于k-mer的病毒序列预测算法
3. GOTTCHA
Genomic Origin Through Taxonomic CHAllenge (GOTTCHA)。把细菌和病毒序列分别识别鉴定出来。
文章：Accurate read-based metagenome characterization using a hierarchical suite of unique signatures
GOTTCHA Github: https://github.com/LANL-Bioinformatics/GOTTCHA
4. ViromeScan
文章：ViromeScan: a new tool for metagenomic viral community profiling
Sourceforge: https://sourceforge.net/projects/viromescan/files/?source=navbar
5. VIP
文章：VIP: an integrated pipeline for metagenomics of virus identification and discovery
描述：Virus Identification Pipeline (VIP)
Github: https://github.com/keylabivdc/VIP
6. MARVEL
文章：MARVEL, a Tool for Prediction of Bacteriophage Sequences in Metagenomic Bins
描述：Metagenomic Analysis and Retrieval of Viral Elements
Github: https://github.com/laboratoriobioinformatica/MARVEL
7. Prophage Hunter
文章：Prophage Hunter: an integrative hunting tool for active prophages
BGI网页工具：https://pro-hunter.bgi.com/index.php/Home/Index/index.html
工具比较：
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