New publications, draft somatic benchmarks, and GIAB analysis call moved to next Monday July 28

[Zook, Justin M. (Fed)]

Dear GIAB analysis team,

 

We are moving today’s call to next Monday, but wanted to share a few exciting updates:

1. Our manuscript “Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair” about HG008 is now published in Scientific Data at https://www.doi.org/10.1038/s41597-025-05438-2. Thanks to many of you who contributed to this!
2. We have new draft v0.4 clonal/truncal somatic SV+CNV benchmarks for HG008. Major improvements include the addition of SVs in VNTRs and large CNVs/CNAs, a new CNV bed file that has the phased copy number for all confident non-subclonal CNV regions, and phasing for most variants in the GTPG field with respect to HG008 normal assembly haplotypes. For more information, see the readme at https://42basepairs.com/browse/web/giab/data_somatic/HG008/Liss_lab/analysis/NIST_HG008-T_somatic-stvar-CNV_DraftBenchmark_V0.4-20250714. As always, we are grateful to receive any feedback you have for improving future versions!
3. We have developed a very preliminary clonal/truncal somatic small variant benchmark for HG008 that we are happy to share if you are interested in helping us evaluate it.
4. We have been iteratively improving near “T2T” assemblies for the tumor and normal cells, which we are happy to share if you are interested in collaborating on analyzing and evaluating these.

If you’re interested in more information about these, you can see the last GIAB call at https://docs.google.com/document/d/18iedHRpmMbdKksiMFfwf3n5O3CpPECzU1VESzmcnXEk/edit?tab=t.0#heading=h.kwvize8u8mt8.

 

We’re postponing this week’s call to next Monday at 1pm EDT, and let us know if you’d like to talk about any of your results next week.

 

Thanks!

Justin

[Zook, Justin M. (Fed)]

Dear GIAB Analysis Team,

 

Just a reminder that we'll be having a GIAB call today at 1pm EDT on 3 topics:

1. Refined tumor/normal assemblies and initial work on polishing
2. Rhyker from Barthel Lab about ordering/orientation of chromosomes
3. Keith from Logsdon Lab about initial analysis of centromeres in assemblies

 

Connection info:
https://nist.zoomgov.com/j/1608716067?pwd=RG1XMVpnTzZYT0J3WTUwQzBGVndJZz09
Meeting ID: 160 871 6067
Passcode: 726592

One tap mobile
+16692545252,,1608716067#,,,,*726592# US (San Jose)

Find your local number: https://nist.zoomgov.com/u/aerqCuhy90

 

Cheers,

Justin

 

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[Zook, Justin M. (Fed)]

Dear GIAB Analysis Team,

 

We'll be having a GIAB call today at 1pm EDT on a few topics:

1. Results of initial polishing of HG008 assemblies
2. Update on potential HG009 cell line
3. Keith Oshima from Logsdon Lab will present the rest of his analysis of centromeres/methylation in HG008 assemblies

 

Connection info:
https://nist.zoomgov.com/j/1608716067?pwd=RG1XMVpnTzZYT0J3WTUwQzBGVndJZz09

Meeting ID: 160 871 6067
Passcode: 726592

One tap mobile
+16692545252,,1608716067#,,,,*726592# US (San Jose)

+16469641167,,1608716067#,,,,*726592# US (US Spanish Line)

Find your local number: https://nist.zoomgov.com/u/aerqCuhy90

 

Cheers,

Justin