tag:blogger.com,1999:blog-36768584.post6311758029146409572..comments2024-03-03T18:49:34.382-05:00Comments on Omics! Omics!: Sequencing's getting so cheap...Keith Robisonhttp://www.blogger.com/profile/04765318239070312590noreply@blogger.comBlogger4125tag:blogger.com,1999:blog-36768584.post-59982991177930302832009-04-20T12:12:00.000-04:002009-04-20T12:12:00.000-04:00The assembly problem can not be overlooked. We did...The assembly problem can not be overlooked. We did a run (SOLiD but the same concern would be for Illumina) of 32 eukaryotic cosmids. They only partially assembled. We did get one full length cosmid and several close to full length. However it seems like the repeat problems in eukaryotes can erase much of the gain of 2nd gen sequencing. Of course that was true with Sanger sequencing as well -- much finishing work was needed.Rickhttps://www.blogger.com/profile/09945270829932237628noreply@blogger.comtag:blogger.com,1999:blog-36768584.post-76006117111468425732009-04-16T10:23:00.000-04:002009-04-16T10:23:00.000-04:00Going from draft to finished is a whole other stor...Going from draft to finished is a whole other story. From what I can gather, draft genomes are still acceptable in eukaryotic sequencing, but not in prokaryotic sequencing. However, you can still have a well assembled draft genome, with big scaffolds assigned to chromosomes. It'll be a draft assembly because of sequencing gaps.RPMhttps://www.blogger.com/profile/00344508931818143159noreply@blogger.comtag:blogger.com,1999:blog-36768584.post-56085992852204331822009-04-16T09:34:00.000-04:002009-04-16T09:34:00.000-04:00That's a good point, and it does moderate the cost...That's a good point, and it does moderate the costs. We were finding costs around $200/plate, but I didn't do the shopping and lower costs are probably doable with volume or relaxed scheduling.<br /><br />I'll admit to being a bit too cavalier about the assembly problem, the consequence of not having been in that trench for a very long time. Going from a draft sequence to finished still remains a big hurdle.Keith Robisonhttps://www.blogger.com/profile/04765318239070312590noreply@blogger.comtag:blogger.com,1999:blog-36768584.post-86916603552761716332009-04-16T06:49:00.000-04:002009-04-16T06:49:00.000-04:00If you search online for DNA sequencing, a common ...<I>If you search online for DNA sequencing, a common advertised cost is $3.50 per Sanger read.</I>That's if you pay by read. It's a lot cheaper if you pay by plate. I think one 96-well plate costs $100-$200. That said, if you're doing de novo transcriptomes, de novo small genomes, or resequencing, paired end Illumina G3 is the way to go (454 is so last year). But if you're doing de novo large genome sequencing (ie, most eukaryotic genomes), you're going to need something else to complement the Illumina sequencing if you want to assemble the genome into good scaffolds.RPMhttps://www.blogger.com/profile/00344508931818143159noreply@blogger.com