Documentation Change History

November 14, 2024

Documentation_v2.13.0

ElemBio Cloud

• Added Compute Connections page.
• Added compute connection information to AWS, DNAnexus, and Seqera provider pages.
• Added ElemBio Cloud 3.4.0 Release Notes.

Bases2Fastq

• Added --group-fastq argument to Optional Arguments.
• Added representative output file structures for grouped FASTQ files.
• Added Bases2Fastq 2.1.0 Release Notes.
• Updated --chemistry-version values in Optional Arguments.
• Updated the version compatibility matrix and the commands for installing a previous version for release of Bases2Fastq v2.1.0.

October 31, 2024

Documentation_v2.12.0

Bases2Fastq

• Updated the version compatibility matrix to support Trinity chemistry.

October 25, 2024

Documentation_v2.11.0

ElemBio Cloud

• Added Data Explorer information to reorganized and updated Data Browsing page.
• Added Data Explorer navigation information to Getting Started.
• Added Use for Data Exploration setting and Manage Data Access button information to Storage Connections and AWS pages.
• Added clarification that braces in file names indicate variability to Run Output.
• Added ElemBio Cloud 3.3.0 Release Notes.
• Moved Bases2Fastq reexecution information to Bases2Fastq Flow.

Bases2Fastq

• Added a second --filter-mask example to Optional Arguments.

Run Manifest

• Added base mask information to run manifest example for reconciling different index sequence lengths.
• Updated Base Mask Settings defaults to reflect currently available sequencing chemistry.

September 25, 2024

Documentation_v2.10.0

ElemBio Cloud

• Added more detailed information on the Amazon HealthOmics options for Bases2Fastq flows.
• Added Verify button information for Managing Flows and permission in Team Member Roles table.
• Added Export button information for the All Runs page.
• Added ElemBio Cloud 3.2.0 Release Notes.
• Updated ElemBio Catalyst Supported Regions to include ca-central-1 and us-east-1.
• Reorganized Bases2Fastq Flow content to move instructions to add a flow to the AWS, DNAnexus, and Seqera provider pages.

August 30, 2024

Documentation_v2.9.0

ElemBio Cloud

• Updated Individually Addressable Lanes add-on information to clarify sequencing kit compatibility.
• Updated Metrics and Charts to clarify availability and source of metrics and charts.
• Updated naming conventions for Cloudbreak Freestyle and Cloudbreak UltraQ.

Bases2Fastq

• Added guidance for testing and downloading simulated data following a Bases2Fastq Installation.
• Updated naming conventions for Cloudbreak Freestyle and Cloudbreak UltraQ.

Run Manifest

• Updated naming conventions for Cloudbreak Freestyle, Cloudbreak UltraQ, and related index sequences.

August 14, 2024

Documentation_v2.8.0

ElemBio Cloud

• Added ElemBio Cloud 3.1.0 Release Notes.
• Added data sharing information for AWS providers and ElemBio Catalyst.
• Added data access management to administrator permissions in the Team Member Roles table.
• Added Keycloak as a compatible IDP for Single Sign-On.
• Updated Advanced Run Settings add-on information for clarity.
• Updated Base Composition to include guidance for low diversity in Read 1.
• Updated and reorganized the AWS provider page to improve clarity.
• Updated naming convention for Cloudbreak Freestyle chemistry throughout the documentation.

Run Manifest

• Updated naming convention for Cloudbreak Freestyle chemistry throughout the documentation.

July 19, 2024

Documentation_v2.7.0

ElemBio Cloud

• Added ElemBio Cloud 3.0.0 Release Notes.
• Updated Data Management download instructions to include more detailed guidance.
• Updated Run Planning to reorganize information into Run Progression section and update run manifest upload step.
• Updated table layout for Run Field Descriptions and Execution Field Descriptions.

Bases2Fastq

• Added Bases2Fastq 2.0.0 Release Notes.
• Added --error-on-missing and --no-error-on-invalid optional arguments.
• Added Missing Invalid or Run Data to the Troubleshooting page.

Run Manifest

• Updated Template Manifests with new Adept and Third Party template and reorganized table for clarity.

June 26, 2024

Documentation_v2.6.0

ElemBio Cloud

• Added Run Output Files information.
• Added Q50 metric and chart information.
• Added Advanced Run Settings add-on information.
• Added Advanced Run Settings add-on configuration information to Add a Planned Run.
• Added a compatibility table to Run Planning.
• Added ElemBio Cloud 2.2.1 Release Notes.
• Updated naming conventions for Cloudbreak Freestyle and Cloudbreak UltraQ chemistry and kits.

Bases2Fastq

• Updated naming conventions for Cloudbreak Freestyle and Cloudbreak UltraQ chemistry and kits.

Run Manifest

• Updated naming conventions for Cloudbreak Freestyle and Cloudbreak UltraQ chemistry and kits.

June 7, 2024

Documentation_v2.5.0

ElemBio Cloud

• Added Trust Relationship policy information for Creating an Execution Role to use with Amazon Health0mics.
• Updated Storage Connections to clarify that information applies to cloud storage connections set up in ElemBio Cloud.

Bases2Fastq

• Added Q scores for 51–56 to the Quality Scores for FASTQ files.
• Added warnings to the Error and Warning Messages table in Troubleshooting.
• Added recommendation to the Operating System matrix to enable WSL 2 if installing Docker on Windows OS.
• Updated Adapter Trimming in Introduction to note passing filter threshold for detection.
• Reorganized links in sidebar to improve Troubleshooting page visibility.

Run Manifest

• Updated Adapter Trimming information for improved clarity.

Tutorials

• Updated Getting Started with Bases2Fastq to reorganize content and incorporate the static binary distribution.

May 17, 2024

Documentation_v2.4.0

Bases2Fastq

• Updated Memory and Performance to specify 2 x 300 AVITI System run requirements.
• Updated Operating System matrix for clarity.
• Updated tabs in Bases2Fastq Installation and Executing Bases2Fastq for functional improvements.

Tutorials

• Updated tabs in Getting Started with Bases2Fastq for clarity and functional improvements.

May 2, 2024

Documentation_v2.3.0

ElemBio Cloud

• Added ElemBio Cloud 2.1.0 Release Notes.
• Updated Data Management to clarify file download information and requirements.
• Updated Run Planning to emphasize cycle distribution flexibility.
• Updated Execution Field Descriptions for new Started By field, Initialized status, and character value clarifications.
• Updated Storage Connections for new settings on storage connection cards.

Bases2Fastq

• Added Troubleshooting page to replace troubleshooting section at the end of Executing Bases2Fastq
• Added information on redundancy of --split-lanes and --legacy-fastq arguments to Optional Arguments.
• Updated Software System and Setup for OS compatibility information and clarity.
• Updated Execution Environments in Introduction for clarity.
• Reorganized Output Files order and added information on FASTQ files without index sequences.

Run Manifest

• Added Reconciling Different Index Sequence Lengths examples.
• Added example to Example Base Masks for a single-index library that requires Index 2 FASTQ files.

April 29, 2024

Documentation_v2.2.0

Bases2Fastq

• Added Bases2Fastq 1.8.0 Release Notes.
• Added a version compatibility matrix for different Bases2Fastq versions.
• Updated --chemistry-version optional argument for forthcoming Cloudbreak UltraQ.
• Updated Output Files for Q50 metrics.
• Updated the sample limit for HTML QC Reports.
• Reorganized Output Files to group metrics files together under one heading.

April 11, 2024

Documentation_v2.1.0

ElemBio Cloud

• Added Access an Example Organization to Getting Started page.
• Updated Indexing Assignment metric information to clarify requirements.

Bases2Fastq

• Reorganized Optional Arguments to use headings for each argument and include example execution commands.
• Removed Example Execution Commands page.

Run Manifest

• Updated Analysis Lane setting to align with availability of the Individually Addressable Lanes add-on.

March 27, 2024

Documentation_v2.0.0

ElemBio Cloud

• Added information for ElemBio Catalyst.
• Added Providers page with pages for Seqera and DNAnexus.
• Added information for Data Management.
• Added Analysis section with information for Executions and Flows, including the Bases2Fastq Flow.
• Added ElemBio Cloud 2.0.0 Release Notes.
• Updated the Run Planning instructions to reflect changes for AVITI OS 2.5.0.
• Updated AWS and GCP information to use them as providers.
• Updated Storage Connections page to focus on storage connection feature and reorganize content.
• Updated Team Member Roles to reflect new features and permissions.
• Moved metrics and charts information to new Metrics and Charts page.

Bases2Fastq

• Added Bases2Fastq 1.7.0 Release Notes.
• Updated --chemistry-version optional argument for Cloudbreak Freestyle.
• Updated --preparation-workflow optional argument for ThirdParty option.

Run Manifest

• Added Cloudbreak Freestyle PhiX Control, Third Party index sequences.
• Updated UmiMask description for default cycles and reads.
• Updated Workflow Summary to use description instead of diagram.
• Removed run manifest templates for v1 chemistry and past AVITI OS versions.
• Removed index sequences for v1 chemistry.
• Reorganized example samples into Examples of Samples page.

Tutorials

• Initial release of Tutorials, including Getting Started with Bases2Fastq and Integrating DNAnexus for FASTQ Automation.

January 16, 2024

Documentation_v1.9.0

ElemBio Cloud

• Added ElemBio Cloud 1.7.0 Release Notes.
• Updated the Run Planning instructions to reflect changes to the order and naming of fields on the Plan a Run form.

November 20, 2023

Documentation_v1.8.0

ElemBio Cloud

• Added table of cycle options to [Run Planning]/docs/elembio-cloud/runs/seq-run-planning/).

Bases2Fastq

• Added guidance for creating HTML QC Reports for Individually Addressable Lanes.
• Added Bases2Fastq 1.6.0 Release Notes.
• Updated Adapter Trimming information for individually addressable lanes.

Run Manifest

• Added Cloudbreak chemistry index sequences for LoopSeq for AVITI.
• Updated Adapter Trimming Settings for use of the plus sign as a delimiter.

November 13, 2023

Documentation_v1.7.0

ElemBio Cloud

• Added Low-Diversity Amplicon Library option to Add a Planned Run.
• Added ElemBio Cloud 1.5.0 Release Notes.
• Reorganized administrator tasks in Managing Team Members, features in Add-Ons, content in Active Runs, and requirements for GCP Storage Connections.

October 26, 2023

Documentation_v1.6.0

ElemBio Cloud

• Added top unassigned sequences to description of Indexing Assignment chart in Run Details.
• Added language to Run Details to clarify when ElemBio Cloud displays specific charts.
• Added ElemBio Cloud 1.4.0 Release Notes.

September 25, 2023

Documentation_v1.5.0

Run Manifest

• Added PhiX Control Library, Adept index sequences for Cloudbreak chemistry.
• Added individually addressable lanes add-on guidance for the Lanes column to Columns and a relevant example to Example Sample Usage.
• Added the Adept Cloudbreak Workflow Run Manifest Template for AVITI OS v2.x to the Template Manifests table.

September 21, 2023

Documentation_v1.4.0

ElemBio Cloud

• Added pages for Run Planning and Add-On Features.
• Added Storage Location Data Upload to Storage Connections page.
• Updated Run Details and Run Field Descriptions for changes in AVITI OS 2.3.0, including new Library Pools field and run planning fields.
• Updated the Active Runs figure for changes to text on active runs cards.
• Updated introduction for Getting Started for new features and diagram of ElemBio Cloud workflow process.
• Updated Inviting Team Members to clarify password prompt for new users and define rules for invitations.
• Revised introduction for Storage Connections for clarity of storage connection processes.
• Reorganized online help navigation menu and updated Platform Navigation to reflect ElemBio Cloud navigation menu.
• Added ElemBio Cloud 1.3.0 Release Notes.

Run Manifest

• Corrected minor typo in Base Mask Settings for the I2Mask default value for Elevate Cloudbreak.

September 6, 2023

Documentation_v1.3.0

ElemBio Cloud

• Added ElemBio Cloud 1.2.0 Release Notes.

Bases2Fastq

• Added Bases2Fastq 1.5.1 Release Notes.

August 14, 2023

Documentation_v1.2.0

ElemBio Cloud

• Added a command prompt to the IAM role creation for setting a 12 hour maximum duration in the AWS CLI.
• Updated IAM role creation for limits on maximum session duration in the AWS Console UI and external ID characters.
• Updated the Release Notes and Change Log to only include ElemBio Cloud Release Notes page.
• Moved Change Log content to Documentation Change History.

Bases2Fastq

• Added project-level file descriptions, metrics, and folder structure to Inputs and Outputs and Output Files.
• Added --filter-mask and --no-projects arguments to Optional Arguments.
• Added Adapter Trimming information to Introduction.
• Added pip3 upgrade information to note in static binary installation instructions
• Added table of time estimates to Memory and Performance.
• Updated Python installation commands in static binary install instructions for accuracy and the Bokeh minor version number.
• Updated Bases file name and quantity in Input Files for change in AVITI OS 2.0.0+.
• Updated Bases2Fastq execution instructions for improved organization and clarity.
• Created Bases2Fastq Release Notes.

Run Manifest

• Added Project column to Columns and Create an Original File.
• Added examples to Base Masks Examples.
• Reorganized Settings page to improve clarity.

July 13, 2023

Documentation_v1.1.0

ElemBio Cloud

• Added descriptions of charts and metrics for AVITI OS 2.2.0 to Run Details and Run Field Descriptions.
• Updated descriptions of Q scores to include confidence rate in Primary Analysis Charts.
• Removed the cycle start information for metrics to direct users to the AVITI OS interface instead.
• Created ElemBio Cloud Release Notes page.

June 16, 2023

Documentation_v1.0.0

Initial release of ElemBio Cloud and the documentation website. Features at launch include the following components:

• Remote run monitoring
• Cloud storage connections
• Team member management