病毒数据分析流程

[anneng]

https://github.com/broadinstitute/viral-ngs

https://github.com/broadinstitute/viral-pipelines

[anneng]

https://www.nature.com/articles/s41598-018-34147-7
Next-Generation Sequencing and Genome Editing in Plant Virology
NGS在植物病毒学中的应用 应用场景包括：
discovery of novel viruses and viroids 发现新病毒和类病毒
detection and identification of those pathogens already known 检测已知病毒
analysis of genome diversity and evolution 基因组多样性和进化分析
study of pathogen epidemiology 病原流行病学研究

[anneng]

https://www.intechopen.com/chapters/49336
Analysis of Next-generation Sequencing Data in Virology - Opportunities and Challenges

[anneng]

http://evbc.uni-jena.de/
欧洲 Virus Bioinformatics center

[anneng]

https://www.broadinstitute.org/viral-genomics/vicuna
组装工具

[anneng]

https://academic.oup.com/nar/article/49/17/e102/6313236
Accurate assembly of minority viral haplotypes from next-generation sequencing through efficient noise reduction

https://github.com/vtsyvina/CliqueSNV
一个病毒单倍型的分析软件 其中第一个步骤是组装

[anneng]

https://github.com/gwcbi/haphpipe
NGS viral assembly and population genetics

[anneng]

https://www.sciencedirect.com/science/article/pii/S0042682216303166
VirusDetect: An automated pipeline for efficient virus discovery using deep sequencing of small RNAs

[anneng]

https://dockstore.org/organizations/BroadInstitute/collections/pgs

[anneng]

Black_washington_0250E_21290.pdf

[anneng]

https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/sars-cov-2-variant-discovery/tutorial.html