Documentation Change History
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-lanesand--legacy-fastqarguments 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-versionoptional 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-versionoptional argument for Cloudbreak FS. - Updated
--preparation-workflowoptional argument forThirdPartyoption.
Run Manifest
- Added Cloudbreak FS 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.
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
Bases2Fastq
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-maskand--no-projectsarguments 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