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From portable to high-throughput benchtop devices, real-time nanopore sensing is a new generation of technology uncovering new biology across multiple sectors.

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Find all the documentation needed for your nanopore experiments, including protocols and device manuals.

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Data Analysis

(15 FAQs)

Where can I find out more about quality scores?What is read alignment?What is genomic sequence assembly?What is basecalling?What is assembly polishing (consensus improvement)?

MinKNOW

Post Run Options

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Why do my reads end up in the “pod5_skip”, “queued_reads” or “tmp” folder?Where is the sequencing_summary.txt file located?Where can I find log files from my sequencing runs?What version of MinKNOW was my .pod5 file generated with?What folder are my reads in?

Adaptive Sampling

(7 FAQs)

Which file formats does MinKNOW expect in order to run adaptive sampling?What is adaptive sampling (formerly referred to as "read until")?What factors affect whether I will see an improvement with adaptive sampling?What can I try if I am not getting my entire region of interest enriched when using adaptive sampling?If I also want to align to my genome of interest when adaptive sampling is on, do I have to specify alignment as well?

Sequencing

(10 FAQs)

What data are in the pings sent to Oxford Nanopore?What are the colours shown in the MinKNOW™ graphs indicating?My screen appears to be frozen or missing features.How to use a sample sheet (.csv or ,json file) to fill out sample names in MinKNOW How much SSD space will my run take up?

Installation and Setup

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What does MinKNOW™ do?I’m connected to the internet but unable to begin sequencing.How to uninstall MinKNOW software for the MinION Mk1B, MinION Mk1D and PromethION 2 Solo devices?How do I upgrade the software on my Device?How do I update my signing key?

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Which file on a workflows github page provides a list of the tools used, their versions, and parameters to run the command?Where can I find the actual code and commands used by the workflows?Where can I find example data files to test the workflows on my computer?Where can I find a list of the expected output for each workflow?The workflow shows in EPI2ME Desktop as completed, but there was no output. What steps should I take next?

Installation and Updating

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What workflows are available on EPI2ME?What internet resources does EPI2ME Desktop need to access?How do I update the application?How do I check the version of EPI2ME Desktop I have installed?Does EPI2ME Desktop need an internet connection?

General EPI2ME FAQS

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What happens to the data on EPI2ME after the analysis is complete?Is the data safe on EPI2ME?

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