Uploading and downloading FASTQ files with BaseSpace CLI

9 December 2020

BaseSpace™ Sequence Hub (BSSH) is the Illumina cloud-based platform for data management, storage, and analysis. In addition to uploading instrument run data, locally generated sample data in the form of demultiplexed FASTQs that meet the file upload requirements can also be imported to a project for use as input for data analysis applications. The BSSH web importer allows for single sample uploads with a maximum size of 250 GB and 16 files per upload. In order to upload multiple samples or larger files, the BaseSpace CLI tool is required to communicate directly through the BSSH API. Note that using BaseSpace CLI requires familiarity with operating in a command line environment. Available for Linux, Windows, and Mac OS X, this tool allows for uploading of data directly to an existing project from the command line. For more information and help getting started with BaseSpace™ CLI, see the links below: Getting Started - BaseSpace™ Command Line Interface (CLI): https://www.youtube.com/watch?v=WLAjo9aT7Ms Support Bulletin - How to use BaseSpace™ CLI to upload FASTQs to BaseSpace Sequence Hub: https://support.illumina.com/bulletins/2018/03/how-to-use-basespace-cli-to-upload-fastqs-to-basespace-sequence-.html BaseSpace™ CLI Overview: https://developer.basespace.illumina.com/docs/content/documentation/cli/cli-overview BaseSpace™ CLI Example Commands: https://developer.basespace.illumina.com/docs/content/documentation/cli/cli-examples Direct Download Links: Linux: https://api.bintray.com/content/basespace/BaseSpaceCLI-EarlyAccess-BIN/latest/\$latest/amd64-linux/bs?bt_package=latest Mac OS: https://api.bintray.com/content/basespace/BaseSpaceCLI-EarlyAccess-BIN/latest/\$latest/amd64-osx/bs?bt_package=latest Windows: https://api.bintray.com/content/basespace/BaseSpaceCLI-EarlyAccess-BIN/latest/\$latest/amd64-windows/bs.exe?bt_package=latest The methods and tools depicted in this video are for research use only and not for use in diagnostic procedures. ©2020 Illumina, Inc. All Rights Reserved. QB #9994 #Illumina #BaseSpace #nextgenerationsequencing A global genomics leader, Illumina provides comprehensive next-generation sequencing solutions to the research, clinical, and applied markets. Illumina technology is responsible for generating more than 90% of the world’s sequencing data.* Through collaborative innovation, Illumina is fueling groundbreaking advancements in oncology, reproductive health, genetic disease, microbiology, agriculture, forensic science, and beyond. *Data calculations on file. Illumina, Inc., 2015. View customer spotlight videos https://www.youtube.com/playlist?list=PLKRu7cmBQlajfheLzgbI4S7xBn7IDbt79 View Illumina webinars https://www.youtube.com/playlist?list=PLKRu7cmBQlahpXlnrrXlQw9itVJ8yHwUZ View Illumina product videos https://www.youtube.com/playlist?list=PLKRu7cmBQlaj6YuZmkfxZcT9twqDgP2Xd View Illumina support videos https://www.youtube.com/playlist?list=PLKRu7cmBQlajbm2KGsICWb-JOnusJfYvM

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