[SIGS Instructions to Authors]
SIGS encourages submission of Standard Operating Procedures (SOPs) for analyzing genomics data when the procedure is part of a routine and repeatable process. The SOPs may include descriptions of fully automated pipelines or combinations of automated and manual steps that are used to produce a data set. SIGS encourages authors of genome reports to reference SOPs used for processing. SIGS aims to provide a repository of best practices in analyzing genomics data and transparency for methods used to produce data in genome reports.
Section headings
Title, Authors, Abstract, Introduction, Requirements, Procedure, Implementation, Discussion
Document types
In order to strike a balance between readability and level of detail, we provide guidelines for SOP documentation at two levels of detail. This distinction between levels occurs entirely within the Procedure section. Both documentation levels should describe a process so that a domain expert can understand the method and process flow. The Level 2 SOP provides additional detail required that would be required to replicate or implement the SOP.
Level 1 SOP:
A general description of the steps in a procedure including listing of software packages used, critical cutoffs, and important decision points. A description of the input and outputs from each step should be provided.
Level 2 SOP:
A detailed description of the procedure that allows for replication or implementation by a domain expert. This description should specifically name relevant software executables and parameters that are necessary for replication of the procedure by an operator of the SOP.
General Guidelines
- The Introduction section should provide the goals and scope of the SOP. Related SOPs can also be referenced in this section.
- Descriptions of software options should be limited to parameters and cutoffs that impact results, deviate from standard defaults, or are commonly customized as part of executing the SOP.
- Troubleshooting information should be provided where appropriate following the relevant steps in the procedure section or more generally described in the Discussion.
- Technical references that are internal to an institution and not public should be excluded. Examples include intranet URLs, file system paths, and computer server names that are not publicly accessible on the Internet.
- A description of the primary output or outputs, including file formats, should be included at the end of the Procedures section or as part of the Implementation section.
- In some cases, an institution will have an SOP that is written and targeted entirely for institution staff rather than the general public. These internal SOPs may contain information only relevant to institution staff, such as file system path or intranet URLs. Before submission to SIGs, we encourage institutions to revise SOPs intended for an internal audience so that are of general interest and are accessible to a wide audience.
Acknowledgements
We would like to gratefully acknowledge the support of many members of the Genomic Standards Consortium, the broader genomic science community, and those who have indicated their willingness to serve as editors, reviewers and contributors.
Funding for SIGS is provided by a grant from the Office of the Vice President for Research and Graduate Studies at Michigan State University, the Michigan State University Foundation, and the US Department of Energy Biological and Environmental Research DE-FG02-08ER64707.
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