Novel Pathogen Detection | ![]() |
DRAGEN Metagenomics App | ||
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Detection and Surveillance | ![]() |
DRAGEN RNA Pathogen Detection App | ![]() |
DRAGEN COVID Lineage App |
Sharing and Collaboration | ![]() |
SRA Import App | ![]() |
GISAID Submission App |
The Illumina SARS-CoV-2 NGS Data Toolkit is available on BaseSpace Sequence Hub. |
The suite of coronavirus software analysis solutions for detection and surveillance of SARS-CoV-2 is free of charge on BaseSpace Sequence Hub, powered by Amazon Web Services (AWS). The toolkit consists of several tools built on the Illumina DRAGEN Bio-IT Platform, and data submission apps on BaseSpace Sequence Hub, which empower researchers to seamlessly submit their findings to public databases.
Illumina SARS-CoV-2 NGS Data Toolkit在不断升级发布新的DRAGEN功能,力求充分利用DRAGEN的速度和准确度来加速对传染性疾病的监测和对病毒爆发的响应。工具包中包含DRAGEN RNA Pathogen Detection Pipeline和DRAGEN Metagenomics Pipeline,分别用于检测传染性疾病和监测病毒的爆发。DRAGEN冠状病毒工具现可在BaseSpace Sequence Hub上获取,从2020年5月起也将在DRAGEN Server上上线。关于利用DRAGEN Platform检测和鉴定冠状病毒的更多信息,请访问此处。
升级版DRAGEN RNA Pipeline现已上线,其利用基于覆盖度和k-mer的方法,进一步加速了高效的病毒病原体检测。新流程适用于任意DRAGEN RNA-Seq Pipeline运行中的SARS-CoV-2检测,无论使用的是哪种应用。新流程的特点包括:
新DRAGEN Metagenomics Pipeline适用于快速简单地检测鸟枪法宏基因组样本中的种属水平。该流程属于宏基因组类的工作流程,能够以高灵敏度和特异性检测和定量SARS-CoV-2序列,同时能提供其他常见病毒和微生物病原体的读数。
该流程利用的是升级后的数据库,其中包含了多种冠状病毒的特异read,流程最后能输出多种类型的结果,包括Krona图、生物检测和QC报告。BaseSpace上的DRAGEN Metagenomics App能够同时分析多个不同样本,赋予了研究人员研究病毒簇的能力。
访问 DRAGEN Metagenomics Pipeline
View sample data generated by this pipeline:
Krona分类图This app aligns reads to a SARS-CoV-2 reference genome and reports coverage of targeted regions. It performs:
对于希望生成SARS-CoV-2临床检测报告来诊断有症状的病人是否患有COVID-19的用户,应该将DRAGEN COVIDSeq Test Pipeline与Illumina COVIDSeq检测结合使用。
对于希望生成鸟枪法宏基因组学测序或Respiratory Virus Oligo Panel临床报告的用户,IDbyDNA提供了简单且强大的生物信息学软件,可将测序仪生成的数据转化为可操作的见解。IDbyDNA经过验证的自动Explify平台分析支持35种呼吸道病毒的检测,包括SARS-CoV-2基因组的鉴定。请致电833-397-5439或发送邮件至clientservices@idbydna.com,联系IDbyDNA客户服务,了解更多信息。
Illumina正在为COVID-19研究团体提供免费的合作环境,帮助研究人员更好的了解调节宿主反应的关键因素并识别潜在疗法的生物标志物。
Correlation Engine如何推动您的研究:
Researchers can process samples using Clarity LIMS. Once sequencing is complete, researchers can automatically stream their data into BaseSpace Sequence Hub using the new toolkit.
Illumina is making it simpler to detect and identify SARS-CoV-2 using NGS with comprehensive, integrated workflows.
Compatible with the Illumina respiratory virus target enrichment workflow, the new toolkit empowers researchers to securely stream data directly off of our full portfolio of sequencers into BaseSpace Sequence Hub for rapid, comprehensive analysis using the DRAGEN RNA Pathogen Detection App. Once analysis is complete, researchers can submit their data to the Global Initiative on Sharing All Influenza Data (GISAID) directly from BaseSpace Sequence Hub.
For researchers looking to enhance their lab efficiency, Clarity LIMS can be used to track and monitor COVID-19 samples, delivering a comprehensive end-to-end solution.
Clarity LIMS Respiratory Virus Panel Workflow
Two new workflows are available for BaseSpace Clarity LIMS:
These new workflows can help ensure samples are viable for analysis – allowing laboratories to quickly start processing coronavirus samples from sample accessioning and library prep to performing QC on sequencing runs.
See this software blog post for additional information about the Clarity LIMS COVID-19 tools.
Access BaseSpace Clarity LIMSExplore NGS methods and find solutions to detect and characterize SARS-CoV-2 and/or other respiratory pathogens, track transmission, study co-infection, and investigate viral evolution.
Learn MoreBaseSpace Sequence Hub旨在支持研究小组之间进行经过审查的安全的协作。通过工作组等团队之间的数据管理和共享功能,您无需下载文件即可安全地与协作者共享项目、开展分析。
The Illumina SARS-CoV-2 NGS Data Toolkit features several BaseSpace Sequence Hub apps for collaboration. The GISAID Submission App accepts a collection of VCF or FASTA files, along with a metadata CSV for the same samples. The app performs data validation before submitting data to GISAID for further QA and processing.
下载BaseSpace安全和隐私信息您可在BaseSpace Sequence Hub上获取完整的Illumina SARS-CoV-2 NGS Data Toolkit。升级版DRAGEN COVID-19工具也将在DRAGEN Server上上线,并将通过DRAGEN API向开发人员开放。*
研究人员现在就可以在BaseSpace Sequence Hub上免费使用Illumina SARS-CoV-2 NGS Data Toolkit,有效期至2020年10月31日。研究人员可以直接将数据从仪器传输到BaseSpace安全的云端环境中,一键式使用整个工具包。
深入了解BaseSpaceBaseSpace Sequence Hub由Amazon Web Services提供支持,您可以利用一套精选的分析应用程序来轻松地管理和分析数据。iCredit是用于购买Illumina基因组数据存储和分析选项的新型货币。
Illumina DRAGEN Bio-IT平台能对测序数据进行准确的超快速二级分析。
NextSeq 2000系统同时支持中通量的新兴应用和外显子测序、靶向富集、单细胞图谱分析、转录组测序等一系列方法。
Understanding host genetic differences and individual responses to the SARS-CoV-2 virus increases understanding of disease susceptibiliity and severity. Read more about the methods for host risk & immune response studies.
Learn MoreDRAGEN Enrichment Pipeline也可用于检测和鉴定SARS-CoV-2。现可在BaseSpace Sequence Hub上以极低的单位样本价格获取该流程,也可从DRAGEN Server上获取。
了解更多*BaseSpace Sequence Hub SARS-CoV-2 NGS Data Toolkit可免费试用6个月,有效期至2020年10月31日。同时,Illumina为COVID-19研究人员提供1年的Clarity LIMS免费试用资格。