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chanzuckerberg / shasta

[MOVED] Moved to paoloshasta/shasta. De novo assembly from Oxford Nanopore reads
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HG004 Truth Assembly Availability #265

Closed janetxinli closed 2 years ago

janetxinli commented 3 years ago

Hello,

I am analyzing several HG004 assemblies and am interested in using the truth assembly as the reference as was done in your paper. The paper states that the assembly should be available in your Google Cloud Bucket (https://console.cloud.google.com/storage/browser/kishwar-helen/truth_assemblies), however I only see data for the other assemblies mentioned in the paper (E. coli, HG00733, etc). Is the HG004 truth assembly still publicly available? If so, where may I find it?

Thank you!

kishwarshafin commented 3 years ago

Hi @janetxinli ,

We did not report the QV value of HG004 as we don't have a high-quality genome assembly available for that sample. We only reported HG002, HG00733 and CHM13:

Screen Shot 2021-08-11 at 3 57 24 PM

Do you want to assess your assembly? Over the last years, there have been several developments in terms of evaluating the assembly. As it does not pertain to this issue, I will not expand. Please feel free to send me an email at shafin@ucsc.edu and I can provide you instructions on how to assess the assembly.

paoloczi commented 2 years ago

I am closing this due lo lack of discussion. Feel free to reopen it or create a new issue if additional questions arise.