I love it! I'm curious about the software side of things, can you say any more? Like, how long did minKNOW take to do its thing and what format were the results? (What sort of file did it end up with?)
minKNOW handled the basecalling in real time, so we could see the reads stream in as the pores worked. the first run lasted a few hours before the flow cell died, second run was i think 12 hours it outputs fast5 (raw signal) and fastq (basecalled reads), which you can feed into downstream analysis tools.
Was literally going to try this when I had a bit more disposable income!! Unfortunate that it’s not quite self-serve yet. I assume you wouldn’t recommend others using your same protocol? Put another, do you think it’s possible to control better for the variables that led to the poor coverage you encountered?
There are a lot of "non-shady" companies which would sequence your DNA for less than $1K. And the amount of data would be tens of Gb. Problem - the data would be in short sequences (100-150 bases). The assembly can be done on a regular PC, using linux.
I love it! I'm curious about the software side of things, can you say any more? Like, how long did minKNOW take to do its thing and what format were the results? (What sort of file did it end up with?)
minKNOW handled the basecalling in real time, so we could see the reads stream in as the pores worked. the first run lasted a few hours before the flow cell died, second run was i think 12 hours it outputs fast5 (raw signal) and fastq (basecalled reads), which you can feed into downstream analysis tools.
Was literally going to try this when I had a bit more disposable income!! Unfortunate that it’s not quite self-serve yet. I assume you wouldn’t recommend others using your same protocol? Put another, do you think it’s possible to control better for the variables that led to the poor coverage you encountered?
a big part was the hardware issue with the flow cell. I think we got a bit unlucky — not yet self serve though.
I bet we could get to 50% coverage next try
Awesome try!
Was rooting for this to work but sad that the coverage and depth ended up so poor.
The protocol often asks for >10000g centrifuge, but you used a tiny one -- was this an issue?
There are a lot of "non-shady" companies which would sequence your DNA for less than $1K. And the amount of data would be tens of Gb. Problem - the data would be in short sequences (100-150 bases). The assembly can be done on a regular PC, using linux.
could be a good tweet