If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
热烈欢迎我们的中国朋友 / A warm welcome to our Chinese friends
Today we are reaching out to the Chinese research community with great news: we are partnering with key companies and institutions in China to empower Chinese researchers to use GATK effectively and at scale.
大家可能已经有所耳闻，我们开发了一整套基因组数据分析系统， 涵盖了分析工具（GATK4，即将发行），流程控制语言（WDL），以及支持多种环境下--包括本地数据中心和云计算--执行分析流程的运行核心Cromwell 。这一整合的套装是为了让生物医药研究人员可以自如的运行、重复分析流程，包括我们一直以来推崇的GATK最佳运行方案（现在我们已经发布了可以即刻使用的流程）。我们希望这一系列努力可以大大减轻之前大家设置以及运行GATK的各种困扰以及烦人的臆测。
As you may know, we have developed a "full stack" genomics solution that combines analysis tools (GATK itself, with version 4 soon to be released), a workflow definition language called WDL, and an execution engine called Cromwell that can execute pipelines in multiple environments, on-premises and on the cloud. This integrated solution aims to empower biomedical researchers to run and replicate analysis pipelines, starting with the GATK Best Practices, for which we are now publishing ready-to-use WDL workflows. We hope this will dramatically cut down on the effort -- and sometimes guesswork! -- previously involved in standing up GATK pipelines.
But our goals didn't stop at just building the pipelining software -- we wanted to make sure our tools would be easy to use on any of the major public clouds. So two years ago, as we were knuckling down to the hard work of developing these software tools, we forged a partnership with six industry leaders who agreed to help us bring our solution to the Cloud -- Intel, Google, Cloudera, Amazon Web Services (AWS), IBM and Microsoft.
Now, we are thrilled that Alibaba Cloud, the major cloud service provider in China, and BGI, the major sequencing service provider, are both signing on to help in the pursuit of our common goal, which is to provide top-quality, reproducible genomics pipelines to everyone in the global research community. It is a happy coincidence that this brings our fellowship of the Cloud to a lucky number eight! We are also engaging with other key companies and institutions in China, including the Beijing Institute of Genomics, Novogene and Inspur, who have expressed interest in adopting our genomics stack.
But that's not all. We're aware that language is often an obstacle for our Chinese audience, so we are looking at options for establishing an outreach program specifically aimed at the Chinese community. This would include a Chinese-language forum, translations of the GATK and WDL documentation, as well as workshops in China. This will be a challenging new undertaking for us but I am optimistic that it will yield great benefits, as I am certain our communities have much to learn from each other.
Finally, I should mention I have personal reasons for being especially pleased that we are reaching out to the Chinese research community in this way. In 2008, I spent several months living and working on a research project at Huazhong Agricultural University in Wuhan, Hubei Province, and I will never forget the wonderful welcome I was given by the staff and students at HZAU. I look forward to finally reciprocating that welcome, at scale!
Photographic evidence… at the 2008 Olympic torch parade in Wuhan!
Many thanks to members of the Intel China team and to Steve Huang of the GATK development team for their invaluable help with the translation!