Complete Khoisan and Bantu genomes from southern Africa : Article : Nature

http://www.nature.com/nature/journal/v463/n7283/full/nature08795.html

Just attended a very good lecture by Stephan Schuster, entitled "African Genomes: Charting Human Diversity"

He offered unbiased views / charts on the platform differences between 454, GAIIx, HiSeq, SOLiD for NGS sequencing coverage (which I think I should not repeat here). It points to the need to do sequencing on 2 different platforms to get a more accurate SNP list.

He also gave compelling reasons for getting a 20x coverage of Human genome done in 454 to complete the human genome (457 gaps in hg19). 

Yes, I often forget that the media / lay person thinks that the human genome is 'complete'. It's a often ignored 'secret' that actually it isn't. Maybe the next marketing ploy(i mean strategy) for emerging sequencing platforms would be to be THE ONE that actually finishes the human genome.

Ion torrent and DNAstar partnership

Ion Torrent to Provide Assembly and Analysis Solutions from DNAStar http://www.genengnews.com/gen-news-highlights/ion-torrent-to-provide-assembly-and-analysis-solutions-from-dnastar/81244638/


Working with commercial software providers appear to be Life Tech's direction. Earlier they announced a partnership with Partek. I think it is a good move since coming up with an inhouse software that works is not enough. There has to be more reasons for using one over another. Unless Life Tech is moving into providing it's own software solutions commercially, it is not cost effective to have a software development team working on solutions. ( unless of course if u r trying to use free software to close the gap between competitors. ) NGS has spawned a demand for bioinfo jobs and software to tackle the deluge of data. With new sequencers and new file formats I think the scene will be still have more vibrant yet confusing times to come.

At ASHG, Ion Torrent Drums Up Interest; Provides Preliminary Specs for PGM

WASHINGTON, DC – Ion Torrent revealed some preliminary specs for its Personal Genome Sequencer, due to be launched later this year, as the Life Technologies business unit presented the instrument to potential customers at its booth at the American Society for Human Genetics meeting this week. The speed of the instrument — a run takes approximately two hours, and several runs can be performed in a day — is what appears to be most attractive to potential customers, Maneesh Jain, Ion Torrent's vice president of marketing and business development, told In Sequence.
The first version of the PGM will sell for $49,500, plus a $16,500 server to analyze the data.
Initially, the machine will produce about 10 megabases of data per run, or about 100,000 reads of 100 base pairs each, using the so-called 314 chip, which has about 1.5 million wells and will cost $250. Reagent kits for template preparation, library preparation, and sequencing will cost another $250, bringing the total consumables cost per run to approximately $500.
In the first half of 2011, Ion Torrent plans to launch the 316 chip, with about 6 million wells, which will increase the output per run to 100 megabases and which will cost about twice as much as the 314. Additional chip upgrades will follow, with details to be revealed next year.
Sample prep, which Jain said takes about a day and can be done in batches of six to eight samples, requires an emulsion PCR protocol, which will be simplified over time. "We focused on the sequencing initially," he said, adding that the next step will be to optimize the sample prep. Life Technologies said previously that sample prep for the PGM would eventually be able to use the EZ Bead system, which was originally developed for the SOLiD system.
Read full article here

AB releases 4 HQ and PI as 5500xl and 5500 SOLiD

Was lucky to be part of the 1st group to view the specs and info on the new SOLiD 4 hq.
For reasons unknown,
They have renamed it to 5500XL and 5500 solid system which is your familiar 4 HQ and PI 
Or if you prefer formulas.
5500xl = 4 hq
5500 = PI

One can only fathom their obession with these 4 digits judging by similar instruments named 
AB Sciex Triple Quad 5500 and the AB Sciex QTrap 5500



Honestly the 5500 numbers are of no numerical significance AFAIK.


outlook wise both  looks like the PI system
I DO NOT see the computer cluster anymore, that's something I am curious about. 

Finally we are at 75 bp though. 
Of notable importance, there is a new Exact Call Chemistry module (ECC) which promises 99.99% accuracy which is optional as it increases the run time. 
the new solid system is co-developed with the Hitachi-Hi Technologies. 
Instead of the familiar slides, they use 'flowchips' now. with 6 individual lanes to allow for more mixing of samples of different reads. 
for the 5500xl
throughput per day is 20-30 Gb 
per run you have 180 Gb or 2.8 B tags (paired ends or mate pairs)


Contrary to most rumours, 5500xl is upgradeable from SOLiD 4 although I suspect it is a trade in program. No mention about the 5500 (which i guess is basically a downgrade).


The specs should be up soon
solid.appliedbiosystems.com/solid5500 




Update from seqanswers from truthseqr 
http://seqanswers.com/forums/showthread.php?t=6761&goto=newpost

Here is the message that has just been posted:
***************
AB is premiering two new instruments at ASHG next week.

Mobile ASHG calendar: http://m.appliedbiosystems.com/ashg/ (http://solid.community.appliedbiosystems.com/)

Twitter account: @SOLiDSequencing (http://twitter.com/SOLiDSequencing)

SOLiD Community: http://solid.community.appliedbiosystems.com/

More info soon at: solid.appliedbiosystems.com/solid5500/ (http://solid.appliedbiosystems.com/solid5500)

ZOMG Life Technologies to Acquire Ion Torrent

6 hours ago Life Tech on their facebook page announced this. I think it's an interesting piece of news considering that Ion Torrent isn't actually selling loads of machines yet. It will be interesting to see how Ion Torrent will fit in with SOLiD and their other slew of sequencing related machines.

Life Technologies Today we announced a definitive agreement to acquire Ion Torrent. Read the details here http://bit.ly/cIzfmq

 

Life Technologies Corporation (NASDAQ: LIFE), a provider of innovative life science solutions, today announced a definitive agreement to acquire Ion Torrent for $375 million in cash and stock.
The sellers are entitled to additional consideration of $350 million in cash and stock upon the achievement of certain technical and time-based milestones through 2012. Life Technologies' Board of Directors has approved an additional share repurchase program in order to repurchase its shares associated with the stock portion of the consideration. The impact on total share count is expected to be neutral. 

UPDATE 
more buzz on the net
http://www.marketwatch.com/story/life-technologies-announces-agreement-to-acquire-ion-torrent-2010-08-17?reflink=MW_news_stmp


Ion Torrent bought by Life Technologies : Genetic Future

Pathogens blog makes an analogy of the sequencing 'zoo'

Lifetech gobbles Ion Torrent: Omics Omics 

Jermdemo thought's on the acquisition