Comments on: Life finds a way

By: dd

dd — Wed, 17 Mar 2010 03:46:59 +0000

SeqDork, you sound like an advertisement for SOLiD. Regarding false positive and false negative rate: it is all a trade off. With either platform you can dial one up, but you are going to pay for it with the other.

By: SeqDork

SeqDork — Wed, 03 Mar 2010 13:44:41 +0000

I believe the BGI deal with ILMN also has similar language with revenues expected over 3 years. Either way you cut it this is great for the industry.
Info I have is 50×35 on paired ends but 50×50 on mate pairs with 75mers coming later in the year.
In terms of Readlength…
Have a look at the 2 Sanger cancer papers (not the same sample..large caveat). Compares genomes with 25×25 on SOLiD V2 vs 75×75 on GAIIx. Similar power to detect variation (appears to have more structure in the SOLiD data with the insert sizes). I think discussions about readlength not anchored in accuracy are smoke and mirror games.

Complete genomics gets alot done with 70 discontiguous 10mers.

Smith et al first demonstrated the lower FP rate in SOLiD data.
Harismendy confirmed this but showed more FNs which from my read is due to comparing Circularized libraries to Fragment libraries.
Walter et al confirms lower FPs with SOLiD in BMC genomics
Clark et al show more power to detect at deprecated coverages with SOLiD than ILMN in U87 PLoS Genetics (caveat..genomic SOLiD to higher coverage array enriched ILMN)
Skryabin et al also has an interesting comparison sequencing the “Russian man” although this looks dated in terms of tech revs.

Likewise Leary et al get alot done with 25×25 in terms of translocation detection with V2 SOLiD

My 2 cents is that everyones opinion on what readlength is needed is influenced by the 75mers they can get (high error) and hence they cant fathom going to 50mers with the same error as mismappings worry them but when they are highly accurate 50mers (8-10X more accurate) alot appears to be getting done.

By: snet

snet — Wed, 24 Feb 2010 15:49:45 +0000

It is confirmed that Ignite is purchasing all 100 units. None of these are planned consignments.

By: dd

dd — Fri, 12 Feb 2010 05:25:49 +0000

MB, you sound like an advertisement for 454.

By: MB

MB — Fri, 12 Feb 2010 04:38:30 +0000

I still think read length matters. 50/35bp is way too short.

By: dd

dd — Mon, 01 Feb 2010 18:35:04 +0000

H. Hare, the Life press release (linked above) says “acquire” in a “partnership” with Life. So it appears there is some wheeling and dealing going on. I have updated the text to be more accurate.

By: H. Hare

H. Hare — Sat, 30 Jan 2010 14:36:41 +0000

Hi David,

I haven’t seen the Ignite release just the Genomeweb story. Did it say purchase or acquire ?