Vertebrate Genomes Project (VGP)

@genomeark

Digital database: near error-free reference genome assemblies for the VGP = all extant 70K vertebrates species

Manhattan, NY
Vrijeme pridruživanja: srpanj 2017.

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    16. sij

    Ensembl 99 and 46 have now been released! 🔸 38 new vertebrate species, 2 dog breeds and 4 updated including from 🔸 New species 🌾🌱🌿 🔸 Updated human variation data 👫 Read more in our latest blog post:

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  3. Closing out VGP Workshop w/Michaela West of + Claudio Ciofi of U Florence Italy sharing their stories as we look to expand the VGP network & group discussion on next steps for completing Phase 1 thanks for joining us!

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    proposes an assembly process that will be evaluated by AI processes that will seek optimal parameters in several steps (e.g. purging duplicates, scaffolding)

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    16. sij

    De novo reference genomes and... ? takes a look towards the future of the VGP and suggests machine learning may play an important role in generating the highest possible quality reference genomes.

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  8. Humans are vertebrates too! gives overview on org + goals for the Human Pangenome Project, which aims to capture the full extent of human diversity from a set of 350 persons

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  9. Biological discovery talks by and on critically endangered species, vaquita (less than 20 remaining) and Great Indian bustard (only 150 remaining), respectively

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  10. TOGO uses genomic context to infer orthologs -> a framework for identifying lost + dup genes; possibility to scale to 100-1000s of genomes. Learn more about its appplication in this paper by presenting author & colleagues

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  11. The afternoon session VGP workshop kicks off w/a talk by Chul Lee about the amount and types of erroneous genes in old and new VGP assemblies, e.g., false gene gains, false gene losses...

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    15. sij

    Listen to for 10 minutes and you’ll never trust a genome assembly again. So ... many ... errors. Great work by her curation team at fixing assemblies and guiding assembly method improvements

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  13. Next, discusses a method for reference free evaluation of genome assemblies - stay tuned for more details in the next couple of months!

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  14. *between HiFi vs...

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  15. Proposal for scalable + cross-platform compatible pipelines by Chai/ to deal with issues of redundancy of effort, reproducibility of platforms, & update speed

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  16. The ongoing assembly problem: repeats are long, spreads are short. compares accuracy vs length between HiFi vs Ultra-long sequencing for human genome assembly

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  17. Sample prep prior to library prep & sequencing vital to final genome!Great presentation by on diff conditions for sample prep incld preservation, tissue types, temps, shipping, DNA extraction, etc for various taxas

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  18. The VGP workshop is getting started w/ giving a quick history leading to current status of ~124 ordinal species in progress & next steps to complete Phase 1 come join us! Terrace room, Handlery Hotel – mjesto: Handlery Hotel San Diego

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  19. UPDATE: our VGP workshop has been relocated to the Terrace room at the Handlery Hotel, start time still 10am

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