General questions
These questions, originally derived for the 16S analysis, relate to other sequencing workflows as well.
Questions related to the nature of the input sequence data
- Were the number, length and quality of the reads obtained in line with what would be expected for the sequencing platform used?
- Was the input dataset of sufficiently good quality to perform the analysis?
- How did the reads’ quality and GC content affect the way analysis was run?
Operational questions
- At each step of the workflow, describe which software was used and why:
- Was the choice affected by the nature and/or quality of the reads?
- Was the choice made due to the time and cost of the analysis?
- What are the accuracy and performance considerations for the chosen piece of software?
- For each software, describe which input parameters were chosen, and why:
- Was the choice affected by the nature and/or quality of the reads?
- Did the available hardware play a role in the parameter choice?
- How did the purpose of the study affect the parameter choice?
- For each step of the workflow, how do you know that it completed successfully and that the results are usable for the next step?
Runtime analysis
This is useful information for making predictions for the clients and collaborators
- How much time, memory, and disk space did each step of the workflow take?
- How did the underlying hardware perform?
- Was it possible to do other things, or run other analyses on the same computer at the same time?
Bibliography
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