The new flow pattern for FLX+

[Zaag]

Has anyone updated their FLX+ machine to 2.8 software with the new flow pattern? Does it work? We are very reluctant, mainly because last time roche touched our machine it nearly died only to come back to live 2 months and numerous replacements later.

Now they claim that some customers have updated and are very happy but they don't show any data. So that is not really promising, specially when you read this thread: http://seqanswers.com/forums/showthread.php?t=26824

Cheers.

[flxlex]

We're pretty happy with the FLX+ now - after more than a year of problems. 2.8 software made a big difference. Roche claims to have amplicon out for FLX+ soon. We are not sure whether it will be 'too little, too late' ('too expensive') to boost interest in the platform much, though...

[Zaag]

Thanks for your answer. That sounds good. I have to say we are happy with the performance of the machine as it is right now, it is quite stable in it 's performance now we have a good protocol. So we don't want to trade longer reads and more output for more variability in readlength and output.

For sequence capture experiments we routinely see these peaks, output can vary between runs but is always >500 MB. Do you think the same kind of stability in peaks and output is possible with the longer reads? Would you be willing to share a runbrowser screenshot of a good FLX+ run?

[Rachael]

Hi Zaag,

Can you confirm the chemistry that was used to generate the above run?

My sequencing facility has the upgraded GSFLX Plus with version 2.8 software and we routinely see the traces similar to yours when using our XLR70 chemistry.

Cheers

[Zaag]

Hi Rachael,

this was a XLR70 chemistry run. Do you see similair peaks (but with higher average length) when running FLX+ kits on your machine?

[Rachael]

The XL Plus sequencing runs we performed (>12 runs) on shotgun and cDNA libraries showed read distributions no better than the XLR70 distributions.

The average read lengths generally were the same and any slight gains in the modal read length was offset by a large amount of small fragments.

We've continued with the XLR70 chemistry which is very reliable and we know that it will be successful when we setup a sequencing run.

Are you running XL Plus chemistry in your lab on your GSFLX Plus machine?

[Zaag]

Ok thanks, that's the sort of information I'm searching for. We did run some XL Plus chemistry but this was with the old flowpattern (2.6 software) and we were not happy with the results because of the things you describe. We got some longer reads but those were accompanied by a lot of shorter ones due to trimming of the reads.

Now Roche claims all this is solved with the new flowpattern (2.8 software), but I'm sceptic and afraid that I have to trade in robustness/reliability for some longer reads and some higher troughput (if any).

Cheers.

[Rachael]

I should clarify, all except 1 of our XL Plus runs was performed with the version 2.6 Software. The 1 XL Plus run we performed with the new flow pattern on version 2.8 showed no improvement in sequencing results.

The v2.8 software upgrade was quite useful for our XLR70 run's because you gain additional information in the GS Run Browser such as "Modal Read Length".

The v2.9 software for Amplicon sequencing is being rolled out in the second quarter of 2013 as well, as per attached Poster available on the my454 website.

[Zaag]

Ok thanks for your answers! I might bug you about IonTorrent in the (near) future.