FLX+ and amplicons

[suefo]

Hi all, I am hoping for a lot of feedback. We don't have a sales rep or application scientist working our region, so I could really use updates on how well the FLX+ upgrades are working with amplicons. Are these supported yet? Are the data better than with the standard FLX runs? Appreciate it.

[RCJK]

Hi there, amplicons are still not supported with the XL+ kits, so you're best bet is to stick to using the XLR70 kits.

[mmoorhouse]

There was some 'mis-communication' about whether the V2.8 upgrade of the Software Pipeline would support Amplicon sequencing at the FLX+ (~700nts-800nts). [The 'Shotgun' mode is for completeness and works quite nicely - when the rest of the reagents work; another separate problem we have had]
I'm sure the people I was talking to at Roche back in May (2012) said that the pipeline would and "be available Q3 2012". So we waited for the upgrade and got ourselves nominated as a test site for it to try it out.
Then when I asked at the start of this month as an update on the release date...no, it was just an instrument control upgrade (mostly) and FLX+ for Amplicons remains unsupported.
So, yes I had misunderstood the contents of the telephone conversation I had with Roche Service in May. I'm very disinclined to believe this actually and more likely given my notes there was miscommunication inside Roche. Whatever.
The ultimate result is the same: FLX+ for Amplicons is unsupported, as per the instrument specifications on the Roche WWW Site.
We for this to change and were thanked politely by Roche for our feedback but no commitment was made etc.

[ajthomas]

This is a bit of a tangent, but please forgive the question--it's not worth a separate thread. From your conversations with Roche, do you know when the version 2.8 software will be available?

[mmoorhouse]

No, not for general release. Asking our wet lab technician I'm told our system is getting upgraded....when our FAS next passes by (usually once a week, but time dependent on our respective other tasks).
We have heard that V 2.8 does offer longer reads but this relates to minor, incremental improvement (I speculate better default parameters resulting in less trimming of the read) rather than full support of the Amplicon at 700nt / FLX+ lengths as discussed in this thread.
Version 2.7 is the latest described on the my454 WWW site with a "Analysis Software Tutorial" so I presume that is the current release. If you want inquire at: [email protected] to Roche directly.

[RCJK]

I'm not sure when v2.8 will be out, but it should be soonish maybe?? I've been told it should improve obtaining longer shotgun reads as there'll be a new reagent flow introduced for XL+ kits based on 8 flows/cycle instead of the standard 4 they've used for ages. I don't think it'll support amplicons though.