James and the Giant Corn Genetics: Studying the Source Code of Nature

January 29, 2010

New SOLiD Sequencers, and the ever dropping cost of sequencing

Filed under: Uncategorized — Tags: , , — James @ 8:20 pm

David Dooling, writing at PolITgenomics, brings word of the announcement of a new generation of SOLiD sequencing machines. The statistics aren’t quite as impressive as the Illumina HiSeq 2000 announced a couple of weeks ago, but it will be cheaper per gigabase of sequence.

As long as SOLiD sequencing can keep giving Illumina a run for its money, the price of sequencing is going to keep dropping, and the R&D departments of both companies will be working round the clock to keep the improvements coming (SOLiD is already promising upgrades that will triple the amount of sequence generated per run, while cutting the cost of each run by half (6x reduction in cost/GB of sequence)… by the end of this year.) (more…)

January 13, 2010

Even Faster Sequencing

Filed under: Fun With Numbers — Tags: , , , — James @ 12:01 pm

Just five years ago in 2005, the state of the art technology for sequencing genomes was Sanger sequencing, the same basic technology that had been used by biologists for decades, although the sequencers of 2005 were the result of decades of refinement of the basic technique. Five years later in 2010, the newest state of the art sequencer is the HiSeq 2000 from Illumina (at least until the Pacific Biosystems sequencers become available later this year… ::drool::). What difference does 5 years make? It would take more than thirty-thousand of the latest and greatest sanger sequencers from 2005 (right before the first next generation sequencer, a 454 machine built by Roche, was released) to produce as much DNA sequence data as a single one of the new HiSeq 2000s produces.* (more…)

December 13, 2009

Panda Genome

Filed under: biology,Genetics — Tags: , , , , — James @ 5:11 pm
Can you imagine how much easier it would be to get funding if you too worked on panda biology?

Can you imagine how much easier it would be to get funding if you too worked on panda biology?

Nature just released a pre-publication copy of a paper detailing the sequencing of the panda genome. The genome was sequenced and assembled using entirely 2nd generation sequencing technologies (specifically the Illumina sequencer) which produced reads that averaged only 53 basepairs long.*

The panda they chose was a three year old female, and they got such resolution (the average individual base pair was sequenced 73 times!) they were even able to identify individual changes in sequence between her two copies of each chromosome.** From this they were able to estimate a difference in the DNA sequence (called a SNP***) occur once every 740 bases which is almost twice the rate of humans. (more…)

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