3 Dec 2021

ORG.one sequencing success (and some oddities)

ORG.one is an initiative from Oxford Nanopore wherein one can apply for free Nanopore consumables for genome sequencing of critically endangered species. Together with a colleague I applied earlier this year, and we were accepted. The sequencing reagents arrived a few weeks ago - two flow cells and one LSK110 sequencing kit. This is the first time I have used the LSK110 kit (until now I have used LSK109), and it seems to work very well. The yields were high, 34 and 37 Gbases, respectively. These flow cells stayed alive for almost a week (with frequent nuclease flushes).  I actually added another 24 hours of sequencing time after 5 days of runtime, and got another ~1.6 Gbase of sequence!

A few oddities during the runs: The translocation speed on the flow cell on our MinION Mk1B was slightly high; starting out just above the green zone. The quality score was also marginally lower than for the other flow cell. 



After 4 days, out of nowhere, reads suddenly began going to the "Skipped" folder. A few hours later this behaviour stopped. I have no idea why. 



The other flow cell was run simultaneously on our Mk1C. After a nuclease flush, suddenly the pores on the sides of the sensor chip no longer worked, and a large proportion of the channels had changed status to "Saturated". However, multiple manual Mux scans gradually brought them back to life. The same happened on every subsequent nuclease flush.