4 ms·
There is a group in UK (Matt Loose's group) that I think is working a lot on read-until. I haven't really kept up with it. I think the key for read-until to wor
by daemonk 9y ago
There is a group in UK (Matt Loose's group) that I think is working a lot on read-until. I haven't really kept up with it. I think the key for read-until to work is ultimately probably going to be better hardware as you need to be able to analyze the trace signal and compare it against a database fast enough to tell the device to kick it out. There are plenty of software optimizations that can be done to compress the signal or extract relevant regions, but the comparison to a database will be difficult to do fast.
- rotexo 9y agoThe computational barriers are definitely an issue. I thought I had read rumors on twitter that ONT was trying to implement read-until on one of their larger-scale sequencers (one of the ones with compute integrated). Barring that, the Cas9-mediated targeting method looks somewhat promising (https://www.youtube.com/watch?v=DGDH-FdoARM https://www.youtube.com/watch?v=DGDH-FdoARM). No need for amplification! Though for applications with human DNA you might run into some issues with the copy number of a sequence of interest if you’re starting out with a normal amount of genomic DNA.
- rotexo 9y agoAlso as a biologist by trade and an audio dsp nut by hobby I loved that they were using algorithms initially developed for music information retrieval to extend the capabilities of a sequencing instrument.