Aviti: Switching Between Element PhiX And Comp PhiX

Generating samplesheets for Aviti sequencing runs often requires specifying the type of PhiX control library used. The Aviti samplesheet generator, by default, uses Standard Element PhiX tags. However, for runs that involve custom primers or other specific experimental setups, Comp PhiX is necessary. Manually editing samplesheets to update the PhiX type, tags, and project can be cumbersome and prone to errors. This article discusses a much-needed feature: a toggle within the Aviti samplesheet generator that allows users to seamlessly switch between Element PhiX and Comp PhiX, ensuring the generated samplesheet automatically includes the correct settings.

Understanding the Need for a PhiX Toggle

PhiX control libraries are essential for ensuring the quality and accuracy of sequencing runs. They act as a balanced control, allowing researchers to monitor the performance of the sequencing process. Standard Element PhiX is the default option, but Comp PhiX is crucial for runs using custom primers. The manual process of switching between these options involves several steps, including updating the PhiX type, associated tags, and project information within the samplesheet. This manual intervention is not only time-consuming but also introduces the risk of human error, potentially leading to failed sequencing runs or inaccurate data. A toggle feature simplifies this process, streamlining the workflow and reducing the likelihood of mistakes. Streamlining this workflow significantly reduces the time and effort required to prepare samplesheets, especially for experiments that frequently switch between standard and custom primer setups. This efficiency gain allows researchers to focus more on their core research activities rather than administrative tasks.

By automating the PhiX selection process, the risk of human error in samplesheet preparation is minimized. Incorrect PhiX settings can lead to sequencing failures or inaccurate results, which can be costly and time-consuming to rectify. Ensuring accuracy from the outset saves valuable resources and maintains the integrity of the research data. A streamlined and accurate process for selecting PhiX controls can contribute to the overall reproducibility of sequencing experiments. Consistent application of the correct settings ensures that data generated across different runs and experiments are comparable and reliable. The inclusion of a PhiX toggle demonstrates a commitment to user-centric design, making the Aviti samplesheet generator more intuitive and user-friendly. This enhances the overall experience for researchers and promotes wider adoption of the platform. The feature ensures that users have the flexibility to adapt their sequencing workflows to specific experimental needs, whether it's using standard protocols or employing custom primer designs. This adaptability is crucial for supporting a wide range of research applications. By simplifying the process of selecting and implementing the appropriate PhiX controls, this feature can help democratize access to advanced sequencing technologies, making them more accessible to researchers with varying levels of expertise. This can accelerate scientific discovery and innovation across diverse fields of study.

User Story: A Streamlined Workflow

The user story highlights the core problem and the desired solution from the user's perspective:

As a user, I want a toggle on the Aviti samplesheet generator Loading page that allows me to choose between Element PhiX and Comp PhiX, so that the samplesheet automatically assigns the correct PhiX type, tags, and project without requiring manual edits.

This user story encapsulates the need for a more efficient and user-friendly experience. It emphasizes the desire to eliminate manual edits and automate the process of assigning the correct PhiX settings. This simple yet powerful feature enhancement can significantly improve the user experience and reduce the potential for errors. The user story clearly articulates the need for a solution that directly addresses the pain points associated with manual samplesheet editing. This focus ensures that the development efforts are aligned with the users' actual needs and priorities. By framing the requirement as a user story, the development team gains a clear understanding of the value that the feature will bring to the end-users. This helps in making informed decisions throughout the development process. A well-defined user story serves as a basis for testing and validation, ensuring that the implemented solution meets the user's expectations and requirements. It provides a specific and measurable goal for the development team to achieve. The user story also helps in prioritizing the development effort, as it clearly outlines the impact of the feature on the user experience and workflow efficiency. This allows for better resource allocation and project planning. Moreover, by focusing on the user's perspective, the user story promotes a customer-centric approach to software development, leading to more intuitive and valuable solutions.

Acceptance Criteria: Defining Success

To ensure the successful implementation of the PhiX toggle feature, specific acceptance criteria have been defined. These criteria outline the requirements that the solution must meet to be considered complete and functional:

• [ ] A toggle or selection field is available on the Aviti Loading page to choose Element PhiX or Comp PhiX.
• [ ] The generated samplesheet automatically populates the correct PhiX type, associated tags, and project based on the selection.
• [ ] If Element PhiX is selected, the standard Element-provided tags are applied.
• [ ] If Comp PhiX is selected, the Comp PhiX tags and associated project are applied.

These acceptance criteria provide a clear and measurable definition of success. They ensure that the implemented feature meets the user's needs and functions as expected. Each criterion addresses a specific aspect of the feature, ensuring comprehensive coverage of the requirements. The availability of a toggle or selection field on the Aviti Loading page is the first critical criterion. This ensures that users can easily access and utilize the feature without navigating through complex menus or settings. Automating the population of the correct PhiX type, tags, and project based on the user's selection is the core functionality of the feature. This eliminates the need for manual edits and reduces the risk of errors. The application of standard Element-provided tags when Element PhiX is selected ensures consistency and adherence to established protocols. This is essential for maintaining the integrity of the sequencing process. Similarly, applying the Comp PhiX tags and associated project when Comp PhiX is selected ensures that the samplesheet is correctly configured for runs using custom primers. These acceptance criteria serve as a checklist during the development and testing phases, ensuring that all requirements are met before the feature is released. This reduces the likelihood of post-release issues and ensures a smooth user experience. Furthermore, these criteria provide a basis for user acceptance testing (UAT), where nominated testers, such as Tris B, can validate that the implemented solution meets their expectations.

Implementation Details and Dependencies

Understanding the implementation details and dependencies is crucial for a smooth development process. This section outlines the technical considerations and potential roadblocks that need to be addressed.

Dependencies

This story is currently blocked by the following dependencies:

• #<issue_no.>
• sanger/#<issue_no.>

Identifying and addressing dependencies early in the development process is essential for preventing delays and ensuring that the feature can be implemented successfully. Dependencies can range from other software components or libraries to external services or APIs. Understanding the nature of these dependencies and their impact on the feature's development timeline is critical for project planning. In this case, the dependencies are represented by issue numbers and repository links, indicating that the completion of this feature is contingent on the resolution of other issues or the availability of specific code changes in a repository. Tracking these dependencies and their status is crucial for maintaining progress and avoiding potential roadblocks. Regular communication and collaboration between the teams responsible for the dependent components are essential for ensuring timely resolution. This may involve coordinating development efforts, sharing updates, and addressing any conflicts or integration challenges. Furthermore, it's important to have a contingency plan in place in case any of the dependencies are delayed or encounter unforeseen issues. This may involve adjusting the development timeline, re-prioritizing tasks, or exploring alternative solutions.

References

This story has a non-blocking relationship with:

• #<issue_no.>
• sanger/#<issue_no.>

Non-blocking relationships indicate that while these issues or code changes are related, they do not prevent the implementation of the PhiX toggle feature. However, it's still important to be aware of these relationships and consider their potential impact. These references may provide additional context, insights, or related functionality that could enhance the PhiX toggle feature. Exploring these references can help the development team make informed decisions and ensure that the feature integrates seamlessly with other components of the system. For example, these references might highlight alternative approaches, potential optimizations, or compatibility considerations. Keeping track of non-blocking relationships helps in maintaining a holistic view of the project and ensuring that all related aspects are considered. This can lead to a more robust and well-integrated solution.

Deployment Notes

Deployment notes are critical for ensuring a smooth and successful release of the new feature. These notes provide specific instructions and considerations for the deployment process, minimizing the risk of issues or disruptions.

Add any details that should be noted when deploying this feature. For example, is a database migration needed, a specific rake task or other script that needs to be run, a dependency on another application or service that needs to be released first, etc?

These notes are intended to ensure the developers releasing the feature know what needs to be done.

Clear and comprehensive deployment notes are essential for ensuring that the feature is deployed correctly and efficiently. These notes should include all the necessary steps, dependencies, and considerations for the deployment process. This may involve database migrations, which are changes to the database schema that need to be applied during deployment. It's crucial to provide detailed instructions on how to execute these migrations and any potential risks or rollback procedures. Specific rake tasks or other scripts may need to be run to configure the feature or perform post-deployment operations. The deployment notes should specify the exact commands to run and any required parameters. If the feature depends on other applications or services, it's important to ensure that these dependencies are released or updated before deploying the PhiX toggle feature. This may involve coordinating deployments across different teams or systems. The deployment notes should also include any known issues or limitations of the feature, as well as any specific monitoring or testing requirements. Providing this information to the deployment team ensures that they are prepared for any potential challenges and can take appropriate action. Furthermore, the deployment notes should include contact information for the developers or subject matter experts who can provide assistance if needed. Clear and accurate deployment notes significantly reduce the risk of errors or issues during the release process, leading to a smoother and more successful deployment.

Conclusion

The addition of a toggle for switching between Standard Element PhiX and Comp PhiX in the Aviti samplesheet generator represents a significant improvement in usability and efficiency. By automating the selection of PhiX settings, this feature reduces manual errors, streamlines workflows, and ultimately empowers researchers to focus on their core scientific objectives. The clear user story, well-defined acceptance criteria, and careful consideration of dependencies and deployment notes ensure that this feature will be a valuable asset to the Aviti sequencing platform. For more information on best practices in sequencing and sample preparation, visit a trusted resource such as Illumina's Sequencing Guides. This will help you stay informed and optimize your research workflows.  Illumina's website offers a wealth of information on various sequencing techniques, sample preparation methods, and best practices. Consulting this resource can help researchers stay informed about the latest advancements in sequencing technology and optimize their experimental designs. By following established guidelines and protocols, researchers can ensure the accuracy and reliability of their results, leading to more meaningful scientific discoveries. Additionally, engaging with resources like Illumina's guides can facilitate a deeper understanding of the underlying principles of sequencing, empowering researchers to troubleshoot issues and adapt their approaches as needed. This proactive engagement with knowledge resources fosters a culture of continuous learning and improvement within the scientific community.