{"id":492,"date":"2022-02-04T17:51:31","date_gmt":"2022-02-04T17:51:31","guid":{"rendered":"https:\/\/terrabioappdev.wpenginepowered.com\/learn-to-assemble-and-analyze-human-pangenome-data-on-the-cloud\/"},"modified":"2023-12-27T04:55:14","modified_gmt":"2023-12-27T04:55:14","slug":"learn-to-assemble-and-analyze-human-pangenome-data-on-the-cloud","status":"publish","type":"post","link":"https:\/\/terra.bio\/learn-to-assemble-and-analyze-human-pangenome-data-on-the-cloud\/","title":{"rendered":"Learn to assemble and analyze Human Pangenome data on the cloud"},"content":{"rendered":"<p><span style=\"font-weight: 400;\">If you missed the <\/span><a href=\"https:\/\/learning.ashg.org\/products\/reproducible-analysis-of-human-pangenome-data-using-the-anvil\"><span style=\"font-weight: 400;\">ASHG workshop on human pangenome analysis<\/span><\/a><span style=\"font-weight: 400;\"> last month, you&#8217;ll be thrilled to hear that the UCSC team uploaded their presentation videos to a <\/span><a href=\"https:\/\/www.youtube.com\/playlist?list=PL6aYJ_0zJ4uA_sbziZu84uas3k0iPlKBx\"><span style=\"font-weight: 400;\">Youtube playlist<\/span><\/a><span style=\"font-weight: 400;\">, so anyone can now learn to analyze pangenomes on the cloud!\u00a0<\/span><\/p>\n<p><span style=\"font-weight: 400;\">The workshop was developed by Dr. Karen Miga&#8217;s team at the <\/span><a href=\"https:\/\/genomics.ucsc.edu\/\"><span style=\"font-weight: 400;\">UCSC Genomics Institute<\/span><\/a><span style=\"font-weight: 400;\">. Dr. Miga leads the <\/span><a href=\"https:\/\/humanpangenome.org\/\"><span style=\"font-weight: 400;\">Human Pangenome Reference Consortium<\/span><\/a><span style=\"font-weight: 400;\"> (HPRC), an exciting collaborative effort that aims to construct a human pangenome reference in order to improve the genomic representation of diverse human populations.\u00a0<\/span><\/p>\n<p><span style=\"font-weight: 400;\">In mid-2021, the HPRC <\/span><a href=\"https:\/\/humanpangenome.org\/year-1-sequencing-data-release\/\"><span style=\"font-weight: 400;\">released a first crop of data<\/span><\/a><span style=\"font-weight: 400;\"> generated from 30 samples using a combination of several sequencing technologies, including long reads. The data is available through several repositories, including the NHGRI&#8217;s <a href=\"http:\/\/anvilproject.org\">AnVIL<\/a>, and can be accessed directly from Terra for analysis.\u00a0<\/span><span style=\"font-weight: 400;\">To facilitate computational reproducibility and reuse of the pangenome resources they produce, the HPRC team shares their data processing workflows via <\/span><a href=\"https:\/\/github.com\/human-pangenomics\/hpp_production_workflows\"><span style=\"font-weight: 400;\">GitHub<\/span><\/a><span style=\"font-weight: 400;\"> and <\/span><a href=\"https:\/\/dockstore.org\/organizations\/HumanPangenome\"><span style=\"font-weight: 400;\">Dockstore<\/span><\/a><span style=\"font-weight: 400;\">. They also provide a <\/span><a href=\"https:\/\/anvil.terra.bio\/#workspaces\/anvil-datastorage\/AnVIL_HPRC\"><span style=\"font-weight: 400;\">Terra\/AnVIL workspace<\/span><\/a><span style=\"font-weight: 400;\"> that bundles the &#8220;Year 1&#8221; data along with preconfigured workflows that can be used to reproduce the full analysis.\u00a0<\/span><\/p>\n<p><span style=\"font-weight: 400;\">The six presentations in the <\/span><a href=\"https:\/\/www.youtube.com\/playlist?list=PL6aYJ_0zJ4uA_sbziZu84uas3k0iPlKBx\"><span style=\"font-weight: 400;\">workshop playlist<\/span><\/a><span style=\"font-weight: 400;\"> provide a comprehensive overview of the project goals and scientific underpinnings, then dive into a series of hands-on demos that show how to use the workflows and workspace in practice (see summaries below). These videos are designed to be accessible to a wide audience, so we encourage you to check them out!<\/span><\/p>\n<p>&nbsp;<\/p>\n<p><iframe title=\"Reproducible Analysis of Human Pangenome Data using AnVIL\" width=\"800\" height=\"450\" src=\"https:\/\/www.youtube.com\/embed\/videoseries?list=PL6aYJ_0zJ4uA_sbziZu84uas3k0iPlKBx\" frameborder=\"0\" allow=\"accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share\" allowfullscreen><\/iframe><\/p>\n<p>&nbsp;<\/p>\n<p><i><span style=\"font-weight: 400;\">Note that accessing the Terra\/AnVIL workspace requires a (free) Terra account. Cloning the workspace and working through the demo for yourself requires a billing account to cover Google Cloud compute costs; free credits are available to fund this. See <\/span><\/i><a href=\"https:\/\/anvilproject.org\/learn\"><i><span style=\"font-weight: 400;\">https:\/\/anvilproject.org\/learn<\/span><\/i><\/a><i><span style=\"font-weight: 400;\"> for more information on getting started with AnVIL resources.<\/span><\/i><\/p>\n<p>&nbsp;<\/p>\n<hr \/>\n<h3><\/h3>\n<h3><span style=\"font-weight: 400;\">Summaries of the <a href=\"https:\/\/www.youtube.com\/playlist?list=PL6aYJ_0zJ4uA_sbziZu84uas3k0iPlKBx\">pangenome workshop playlist<\/a> videos:<\/span><\/h3>\n<p>&nbsp;<\/p>\n<p><strong><a href=\"https:\/\/www.youtube.com\/watch?v=8pqPhmDOm6k&amp;list=PL6aYJ_0zJ4uA_sbziZu84uas3k0iPlKBx&amp;index=1\"> Introduction to the Human Pangenome Reference<\/a><\/strong><\/p>\n<p><span style=\"font-weight: 400;\">Introduction to the goals of the project, how the consortium is sharing their results early and often, and the currently available data from Year 1. \u2014 Karen Miga, Director of the Human Pangenome Reference Consortium<\/span><\/p>\n<p>&nbsp;<\/p>\n<p><strong><a href=\"https:\/\/www.youtube.com\/watch?v=4b7mBb093j4&amp;list=PL6aYJ_0zJ4uA_sbziZu84uas3k0iPlKBx&amp;index=2\"> Introduction to AnVIL and how it supports HPRC<\/a><\/strong><\/p>\n<p><span style=\"font-weight: 400;\">A brief introduction to the NHGRI AnVIL ecosystem and what it offers to data scientists, including an example of how the Human Pangenome Reference Consortium is leveraging AnVIL for transparent science. \u2014 Beth Sheets, Program Manager<\/span><\/p>\n<p>&nbsp;<\/p>\n<p><strong><a href=\"https:\/\/www.youtube.com\/watch?v=mN4m_e85CLo&amp;list=PL6aYJ_0zJ4uA_sbziZu84uas3k0iPlKBx&amp;index=3\"> Exploring and Accessing HPRC Data Resources in AnVIL<\/a><\/strong><\/p>\n<p><span style=\"font-weight: 400;\">Demo of how to find, explore, and access data from Year 1 from the Human Pangenome Reference Consortium on AnVIL. Data can currently be accessed in <\/span><a href=\"https:\/\/anvil.terra.bio\/#workspaces\/anvil-datastorage\/AnVIL_HPRC\"><span style=\"font-weight: 400;\">this AnVIL\/Terra workspace<\/span><\/a><span style=\"font-weight: 400;\"> (requires a Terra account). \u2014 Julian Lucas, Bioinformatics Systems Analyst<\/span><\/p>\n<p>&nbsp;<\/p>\n<p><strong><a href=\"https:\/\/www.youtube.com\/watch?v=fxXGvfIr4dY&amp;list=PL6aYJ_0zJ4uA_sbziZu84uas3k0iPlKBx&amp;index=4\"> Introduction to Genomic Workflows from HPRC<\/a><\/strong><\/p>\n<p><span style=\"font-weight: 400;\">Introduction to Genomic Workflows written in the Workflow Description Language (WDL) that can be launched in the NHGRI AnVIL cloud ecosystem. Covers the following topics: Why use containers and workflow languages; How to build a container; How to write a workflow in the Workflow Description Language (WDL); and Tools for testing your WDL workflow. \u2014 Trevor Pesout, PhD Candidate<\/span><\/p>\n<p>&nbsp;<\/p>\n<p><strong><a href=\"https:\/\/www.youtube.com\/watch?v=c8CkGHextog&amp;list=PL6aYJ_0zJ4uA_sbziZu84uas3k0iPlKBx&amp;index=5\"> A Demo of Running The HPRC Assembly Workflow in AnVIL<\/a><\/strong><\/p>\n<p><span style=\"font-weight: 400;\">Introduction and demo of an assembly workflow that has been developed and used to build a reference that will be included in the Human Pangenome. The video demonstrates: Where to find the workflow in Dockstore; How to launch the workflow from Dockstore into AnVIL&#8217;s Terra environment; The types of data needed and how to set up data input for the workflow; and How to find, view, and download output files from the workflow. \u2014 Mobin Asri, PhD Candidate<\/span><\/p>\n<p>&nbsp;<\/p>\n<p><strong><a href=\"https:\/\/www.youtube.com\/watch?v=1i5TxvESmNY&amp;list=PL6aYJ_0zJ4uA_sbziZu84uas3k0iPlKBx&amp;index=6\"> Calling Variants with a Pangenome in AnVIL<\/a><\/strong><\/p>\n<p><span style=\"font-weight: 400;\">Introduction to pangenomes and demo of variant calling using Giraffe and DeepVariant tools with a pangenome reference in AnVIL (see <a href=\"https:\/\/anvil.terra.bio\/#workspaces\/cgp-terra-outreach-workshop\/Human-Pangenome-Giraffe-DeepVariant-AnVIL-ASHG-Jan22\">this AnVIL\/Terra workspace<\/a>). \u2014 Julian Lucas, Bioinformatics Systems Analyst<\/span><\/p>\n<p>&nbsp;<\/p>\n<p>&nbsp;<\/p>\n","protected":false},"excerpt":{"rendered":"<p>A new playlist of workshop videos by Dr. Karen Miga&#8217;s team at UCSC demonstrates how to use data and resources from the Human Pangenome Reference Consortium<\/p>\n","protected":false},"author":4,"featured_media":493,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":""},"categories":[18,31,106,53,37,119,38,39,32,40,14],"tags":[41,172],"class_list":["post-492","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-data","category-ecosystem","category-genomics","category-getting-started","category-medical-and-population-genetics","category-most-recent","category-tutorials","category-videos","category-workflows","category-workshops","category-workspaces","tag-anvil","tag-pangenome"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.0 - 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