Has anyone got their hands on a v3 MiSeq kit and run some samples yet?
-
-
Josh Quick (@Scalene) has Tweeted some quality & intensity plots from 300 cycle runs (presumably using the new kits)
-
I'd love to see the Qscore plot on that run. Excited for amplicon sequencing to see it move out to 2x300. Anyone know the expected release date for said kit (Though I guess that was the question of the OP!)?Comment
-
Someone who would know told me:
PS they're on iCom nowTechnically the MiSeq v3 are available to order. They should be on iCom
this week.
They will probably start shipping latter this week or early next week.
The cost is 1400 for 2x300 and 800 for 2x150.
PPS although it looks like PE75, not PE150, as it's only a 150 cycle kit.Last edited by GW_OK; 08-20-2013, 06:50 AM.Comment
-
MiSeq updater (v.2.3.0.8) is available now on iCom, probably required for for v.3 kits.Comment
-
$1400 for a 600 cycle kit is a big jump from $1050 for a 500 cycle. Yeah they say you can get 25M reads vs the 15M for the v2 kits, but that still seems like quite a jump.
Those intensity plots sure are different though..
BTW, anyone have issues installing the MCS update? I tried to install the update, seemed to go fine, system rebooted, and then it comes up asking me to repair the install. This then fails on an error related to the BaseSpace broker. Will probably give tech support a call in a few to see what they say.
-- Well, after exiting the fix installation bit and rebooting, MCS eventually came up after showing only a black screen for a good 5 minutes. All software versions are now current, so I'm guessing the update worked. Might be an issues with BaseSpaceBroker since it's included in the upgrade software but nothing is actually changing about it.Last edited by mcnelson.phd; 08-20-2013, 11:54 AM.Comment
-
The cycling times are a lot longer too. It's 65 hours for a 2x300bp run! That won't help with the backlog at most sequencing cores.Comment
-
Well they are sequencing a larger area of the flowcell. They're going from ~12.8 cycles/hour to ~9.2 according to their posted run times. It'd be nice to see v3 micro and nano kits, or even v3 chemistry with v2 real estate, for people who need read length but not a lot of reads. That'd be good competition for Ion Torrent.Comment
-
Are you still getting the issues launching MCS? Even after a restart I am getting similar problems and can not get any of the Illumina programs to launch. I guess I will be calling tech support tomorrow too.Originally posted by mcnelson.phd View PostComment
-
-
"According to the company, the new kit will enable new applications on the MiSeq such as exome sequencing and transcriptome sequencing."
With 80% of exons being <200 bp (ave 170 bp), does Illumina really think PE-300 is suitable for exome sequencing? They use the 15 Gb yield of PE-300 and make it sound like it is possible (300bp*2*25M=15 Gb), but I would need ~2X more reads and PE-75 or PE-100 to do a 100X exome. The PE-300 is better suited for amplicon and genome than exome and transcriptome. We'll have to fragment cDNA to get long enough fragments to do a PE-300 RNA-seq library, currently with TruSeq it is hard to get >150-300 bp fragments with 0-1 minutes fragmentation. Possibly good for long reads for de novo RNA-seq? Expensive 15M run for just counting. 25M PE-100 reads ok for reduced exome focused on most relevant Refseq sites?Last edited by epistatic; 08-20-2013, 02:51 PM.Comment
-
No, the edit I added later noted that after I restarted the whole system MCS eventually came up. I won't be able to try a run for a few days though since we're having optical issues that will require someone to come check things, so there may be some gremlins left to cause issues.Originally posted by gblanchard4 View Post
I have had an issue with my MiSeq Reporter install off-instrument not updating, so I'll have to look into that more tomorrow.
After looking through the MCS update notes though, it looks like Illumina is being pretty bullish on expanding the range of applications for the MiSeq. Amplicon-DS workflows and read "stitching" options in Reporter point to a big focus on amplicon sequencing. With 25M reads at 2x300bp, it looks like there's absolutely no reason to ever run a 454 again.Comment
-
The v3 reagent kits are available to buy on the illumina website, but I'm not able to download the new software yet in the UK. Think I'll wait a while anyway before I upgrade to make sure any problems have been ironed out!Comment
-
I just upgraded a MiSeq to the new version of MCS. No surprises or odd behavior. Took less than 10 minutes and a single reboot.Comment
-
Seems kind of odd that they don't have a 2x150bp v3 kit. I think that's the one we use around here by far for routine applications and it has a sweet spot in terms of amount of data and run time. If we assume that it takes half the time as the 2x300, then 33 hours is not too bad at all.Comment
-
NGS has revolutionized clinical microbiology by offering new ways to identify and surveil pathogens without prior knowledge of the target. One popular approach is 16S rRNA and ITS amplicon sequencing, which targets specific microbial markers. But studies are increasingly incorporating shotgun metagenomics, a technique that sequences all DNA from a sample without targeting specific microbial markers. This approach allows more detailed taxonomic classification, detection...Today, 06:46 AM -
Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?
Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating...10-14-2026, 09:55 AM
Comment