Scope
Important
This section is a fundamental building block of any SOP
The ‘Scope’ section of an SOP should define the boundaries of the procedure i.e. what it covers, what it excludes, and who it applies to. It ensures that users understand the exact context and applicability of the procedure, helping to prevent misuse or misinterpretation.
Depending on the type of procedure being documented, the scope may include:
Types of data or samples: The specific data formats, sample types, equipment, or materials the procedure is designed for.
Technologies and methods: The platforms, tools, or methodologies the procedure applies to.
Personnel: The roles or individuals authorised to perform or oversee the procedure.
Limitations: Any exclusions, constraints, or unsupported scenarios users should be aware of.
Example content:
🧬 Bioinformatics QC Procedure
Example content from a bioinformatics SOP outlining the procedure for assessing the quality of Illumina sequencing data prior to downstream bioinformatics analyses.
Scope
This SOP applies to the quality control of 150bp paired-end FASTQ files generated using Illumina sequencing instruments (e.g. MiSeq, NextSeq) for microbial datasets only. This SOP does not cover:
Quality control of non-microbial datasets;
Sequencing performed using alternative read lengths, library preparation workflows or non-Illumina platforms (e.g. Pac-Bio or Oxford Nanopore); or
Downstream bioinformatic analyses beyond the initial QC evaluation.
👩🔬 Staff Training Procedure
Example content from an SOP outlining a training procedure
Scope
This SOP applies to all internal training activities conducted within ISO-in-a-Box, including skills development for staff, interns, and collaborators working under the project’s quality system. It covers:
Planning and preparing training sessions
Delivering training using the Tell–Show–Do–Apply model
Supervising trainee practice
Conducting competency assessments
Documenting training activities and maintaining training records
This SOP does not cover:
External workshops or regional/international training events
Platform-specific or topic-specific procedures (covered by their own SOPs)
Formal certification or accreditation programmes delivered by external bodies
Human resources onboarding processes
🌌 Galaxy Training Procedure
Example content from a training SOP detailing the standardised procedure for training on the Galaxy platform
Scope
This SOP applies to all staff involved with aspects of training (trainers and trainees) related to building, executing, and managing analysis workflows within the Galaxy platform. It covers the training and competency assessment process for navigating the Galaxy interface, selecting and configuring tools, creating and editing workflows, running workflows on provided datasets, and documenting workflow parameters and outputs.
This SOP does not cover advanced Galaxy administration tasks such as server configuration, tool installation, user permission management, or development of custom tools. It also excludes downstream interpretation of scientific results beyond verifying workflow functionality.
The procedures described herein apply to training activities conducted within the institution’s designated Galaxy environment and are intended for users with basic familiarity with biological data formats but no prior experience with workflow construction.
🧪 Laboratory Procedure
Example content from a wet-lab SOP outlining the procedure for preparing sequencing libraries using the Illumina DNA Prep kit.
Scope
This SOP applies to the preparation of sequencing libraries using the Illumina DNA Prep Library Preparation Kit within the laboratory and covers the preparation of libraries from DNA (including cDNA generated from RNA) derived from microbial samples for sequencing on Illumina platforms.
This SOP does not cover:
DNA extraction or other upstream sample processing steps.
Library preparation for alternative sequencing platforms (e.g. Oxford Nanopore Technologies, PacBio).
Library preparation using Illumina kits other than the Illumina DNA Prep Library Preparation Kit.
💻 Code Update & Review Procedure
Example content from an SOP outlining the procedure for updating and reviewing code within the Luma Genomics Unit (LGU).
Scope
This SOP is primarily concerned with ensuring that changes to software are authorised, moderated and reviewed to ensure consistency with organisational policies on coding style. The following related processes are covered by other SOPs and are not covered here:
Validation and verification of software and pipelines
Development and tracking of coding competencies