What is the sequence of steps that happen when sequencing with Oxford Nanopore MinION to get the nucleotide sequences? Do users have direct access to the nucleotides from the sequencer in their laptops? Or do the signals get sent to the Nanopore servers, which then translate them to nucleotide sequences?
You get signals on your computer indicating voltages per pore. Then your computer uploads them to Oxford Nanopore, where they use non-public software to do base-calling, and generate a non-standard file. You can then use unsupported 3rd-party programs to pull fastqs out of this file, which are usable by mainstream software. It's very straightforward, and only involves storing and uploading about 1000 bytes to the internet per called base, so it's very efficient and secure as well.
P.S. This information is a few months old; I'm certain that the process has become even more streamlined since then!
Oxford Nanopore uses the 'fast5' format which you can access if you want to process the raw data yourself.
Check out this paper's methods where they do their own signal correction and base calling using their own software package called Poretools (documentation | paper). It's the best way to do it at the moment as far as I am aware.
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Thank you Brian. Do you know if there is anything preventing software developers from writing their own base-calling software? Instead of going to the Oxford Nanopore cloud, what are things preventing writing base-calling software on one's private computer/cluster?
There is nothing preventing you... in my opinion, Oxford's goal is to encourage the development of better base-callers, and they would be happy to see them.