Diagnostic Sequencing —
Training activity: 2

Details

Generate a genomic sequence alignment in an appropriate format

Type

Developmental training activity (DTA)

Evidence requirements

Evidence the activity has been undertaken by the trainee​.

Reflection on the activity at one or more time points after the event including learning from the activity and/or areas of the trainees practice for development.

An action plan to implement learning and/or to address skills or knowledge gaps identified.

Reflective practice guidance

The guidance below is provided to support reflection at different time points, providing you with questions to aid you to reflect for this training activity. They are provided for guidance and should not be considered as a mandatory checklist. Trainees should not be expected to provide answers to each of the guidance questions listed.

Before action

What are the intended outcomes of the training activity?

• How does the process of generating a genomic sequence alignment in an appropriate format (e.g., BAM) help you explain the structure of the human genome and the impact of variation on human development and disease?
• In what ways will you evaluate sources of information regarding variation, specifically focusing on their access, application, and clinical impact during this task?
• What criteria are you using to select the most appropriate NGS tools for the analysis of the inherited or acquired disease associated with this dataset?
• How will you ensure that you are successfully analysing NGS data in a clinical setting by applying the necessary quality control and data validation steps?
• What specific reference genome version and metrics, such as a target mapping rate, have you identified as the thresholds for a ‘successful’ alignment?

What do you anticipate you will learn from the experience?

• What specific insights do you hope to gain concerning the impact of alignment parameters on the resulting clinical data?
• Based on what you already know about the concepts of mapping reads to a reference genome, what do you expect to learn about the nuances of different alignment algorithms, such as those for short-read versus long-read data?
• What do you anticipate learning about the computational resource requirements and data handling complexities associated with large-scale genomic datasets?

What actions will you take in preparation for the experience?

• Have you discussed the activity with your Training Officer to ensure you have a clear understanding of the software expectations and the definition of success for this specific task?
• What preparation have you done to handle potential challenges, such as troubleshooting persistent error messages or managing complex genomic regions like repetitive sequences?
• Have you reviewed the relevant Standard Operating Procedures (SOPs) and best practice guidelines to confirm you understand sample-specific requirements, such as paired-end reads or library types?
• If your previous attempts at generating alignments were problematic, what specific plans have you put in place to address the causes of those issues this time?
• How do you feel about embarking on this training activity, and can you clearly identify the point at which an issue would fall outside your scope of practice, requiring you to seek immediate advice or help?

In action

What are you doing?

• How are you approaching the activity of mapping reads to a reference genome, and why have you chosen this specific workflow or pipeline for this inherited or acquired disease?
• As you generate the alignment, what specific decisions are you making regarding alignment parameters or the selection of the reference genome version?
• How are you evaluating the sources of information used during this process, particularly regarding their clinical impact and application to the dataset?
• What aspects of generating a BAM file and managing its format feel intuitive to you, and which parts require more conscious effort, such as explaining how the resulting alignment reflects the structure of the human genome?

How are you progressing with the activity?

• How effective are your current actions in achieving a successful alignment, and are you meeting the expected criteria, such as a high mapping rate?
• Are you facing any immediate challenges, such as the process taking significantly longer than expected, the software producing unexpected error messages, or dealing with complex genomic regions like repetitive sequences?
• What can you learn from this activity as it unfolds about the relationship between raw sequencing data and the impact of variation on human health?
• How does the current data you are processing connect to your existing skills in analysing NGS data and applying quality control?

How are you adapting to the situation?

• If you encounter a low mapping rate or a software crash, what alternative approaches, such as adjusting parameters or using a different alignment algorithm, are you considering?
• What specific support or guidance do you need in this moment if you find it difficult to troubleshoot a persistent error or interpret a complex quality metric?
• Are you working within your scope of practice, and can you identify the exact point at which a technical issue—such as a fundamental bioinformatic flaw—requires you to seek immediate advice from a specialist?
• How are you adjusting your strategy if the computational resource requirements for this specific clinical dataset exceed what you initially anticipated?

On action

What did you notice?

• How would you summarise the key steps involved in generating the genomic sequence alignment, and which specific tools or software did you utilise to complete the task?
• Were the input and output formats (such as BAM or SAM) appropriate for the analysis, and did you observe any specific events, actions, or interactions during the process that felt particularly important?
• Did you notice any unexpected discrepancies between your prepared plan and the actual alignment results, such as a surprising mapping rate or specific software errors?

What did you learn from the activity?

• What specific knowledge did you improve regarding the structure of the human genome and the way variation within it impacts human development or disease?
• How did this experience enhance your ability to evaluate sources of genomic information and their clinical impact when preparing your alignment?
• What strengths did you demonstrate in selecting the appropriate NGS tools for the inherited or acquired disease context, and what gaps in your knowledge were revealed?
• In what ways did you successfully analyse NGS data in a clinical setting while applying appropriate quality control and data validation?
• How did your reflection-in-action (decisions made during the task) influence the eventual outcome, particularly when dealing with complex regions or computational issues?
• How did this experience compare to previous alignment tasks, and do you feel your practice in handling large genomic files has improved?

What will you take from the experience moving forward?

• What specific areas for continued development have you identified, such as a need to better understand different alignment algorithms or specific output flags?
• How can you apply the learning from this activity—specifically regarding tool selection and data validation—to your routine clinical practice?
• What are the clear next steps you will take based on this experience, such as practicing with specific alignment formats or refining your troubleshooting strategies?
• What additional support or resources (e.g., specialist advice on computational optimisation) might you need to further develop your skills in this area?
• How has this activity changed your perspective on what you would do if faced with similar technical challenges in a future clinical analysis?

Beyond action

Have you revisited the experiences?

• How have you evaluated and re-evaluated your reflections from various instances of generating genomic sequence alignments, particularly those involving challenging data such as indels or repetitive regions?
• When comparing your performance in this training activity to Observed Training Activities (OTAs), what specific observable behaviours or professional practices have you successfully assimilated into your routine work?
• Through professional storytelling with peers or senior colleagues, how has your view of alignment strategies transformed, and have these discussions changed your approach to complex clinical datasets?
• Have you reviewed your notes on previous alignment attempts to confirm you are now consistently applying refined techniques to address the impact of variation on human development and disease?

How have these experiences impacted upon your current practice?

• How has the accumulation of experiences in performing sequence alignments across multiple datasets refined your efficiency and skill in this area?
• In what ways have you applied your improved ability to evaluate sources of information and select appropriate NGS tools to other training activities or clinical reports?
• How has this cumulative learning prepared you for formal assessments, such as the Direct Observation of Practical Skills (DOPS) where you must view a sequence alignment BAM file and assess variants or structural changes?
• How do you now integrate your knowledge of quality control and data validation when moving from raw sequence data to clinical interpretation in your daily workflow?

How might these experiences contribute towards your future practice?

• What transferable skills have you developed through this activity—such as computational troubleshooting or data management—that will support your wider practice as a Clinical Bioinformatician?
• Based on your repeated practice, can you now more readily identify when a genomic alignment task is particularly complex and potentially beyond your current scope of practice, requiring escalation or specialist advice?
• What clear actions have you identified for the continued development of your skills, such as mastering new alignment algorithms for different disease contexts or emerging sequencing technologies?
• How has your developing expertise in genomic alignment influenced your ability to contribute to multidisciplinary team (MDT) discussions regarding the clinical impact of identified variations?

Relevant learning outcomes

#	Outcome
# 1	Outcome Explain the structure of the human genome and the impact of variation on human development, health, and disease.
# 2	Outcome Evaluate sources of information about variation in the human genome including access, application and clinical impact.
# 3	Outcome Select appropriate tools for next generation sequencing (NGS) analysis of inherited and acquired disease.
# 4	Outcome Analyse NGS data in a clinical setting applying appropriate quality control and data validation.