Many of our benchmarks are derived using the default cut-offs used in MinKNOW. As such, generally, the pass data obtained from MinKNOW should be appropriate for your analysis.
Individual applications may have specific recommendations, and we would recommend reading the latest best practice workflows available on the Applications page or the relevant workflows described in our analysis platform, EPI2ME Labs or EPI2ME.
Other third-party workflows may have requirements different from the defaults available through MinKNOW.
Should you need to filter data, there are a number of tools for filtering read data such as Filtlong.
For third-party tools, please see their GitHub pages for installation and usage. To address any issues with these and other third-party tools, please post to the “Issues” tab on the individual GitHub repositories as we cannot offer support for third-party software.