tag:blogger.com,1999:blog-36768584.post2286899806625870542..comments2024-03-03T18:49:34.382-05:00Comments on Omics! Omics!: New Life in the Sanger MarketKeith Robisonhttp://www.blogger.com/profile/04765318239070312590noreply@blogger.comBlogger6125tag:blogger.com,1999:blog-36768584.post-72263633772155994312017-07-20T09:02:36.853-04:002017-07-20T09:02:36.853-04:00That's bare run costs, and the library prep co...That's bare run costs, and the library prep costs are in the area for 30-100$ per sample...<br /><br />Also don't forget bioinformatics costs (not all users know how to prepare a bam file from their custom vector reference and run reads and call the variants).<br /><br />Also prices in the Europe/UK are a lot higher for most users of the Illumina MiSeq kits.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-36370827205343943112017-06-20T02:10:07.873-04:002017-06-20T02:10:07.873-04:00I wonder if it has to do with a lack of awareness ...I wonder if it has to do with a lack of awareness of the sequencing kits that are out there.<br /><br />A Miseq Nano 300 cycle kit runs for ~$240 and ~$290 for a 500 cycle kit, including our institutional discount. This gives you about a million reads. You can fragment at least 10 plasmids with fragmentase or even plain old nonunique restriction enzymes and get a really high quality sequence assembly in less than a day. You can do the same for sequencing larger amplicons.<br />billytclhttps://www.blogger.com/profile/03608858369795586009noreply@blogger.comtag:blogger.com,1999:blog-36768584.post-79438423171468149082017-06-16T09:49:42.943-04:002017-06-16T09:49:42.943-04:00It is hard to beat Sanger on low throughput low co...It is hard to beat Sanger on low throughput low cost sequencing. Library construction costs are a concern for any other method. We do have a service that offers 2nd gen sequencing for $25/sample (Univeristy price) with enough coverage for plasmid size samples. Some people have pushed this up to BAC-size (120 Kbase). However being 2nd gen (miSeq/hiSeq) there is assembly involved which, of course, can be problematic. We have had some very nice results and then some poorer results.<br />Rickhttps://www.blogger.com/profile/09945270829932237628noreply@blogger.comtag:blogger.com,1999:blog-36768584.post-63589580997752920572017-06-16T00:03:49.366-04:002017-06-16T00:03:49.366-04:00The MinION is remotely competitive, particularly i...The MinION is remotely competitive, particularly if you're sequencing lots of sequences of different lengths (or sequences that are easily separable in post). Consider that 12 samples with 10 different 1-10kb amplicons per sample will have a marginal reagent cost of about $6 per sequence (after the DNA is extracted/amplified), and that's assuming the flow cell is not washed and re-used.<br /><br />Consensus quality is an issue for MinION, but cost doesn't need to be.David Eccleshttps://www.blogger.com/profile/11754558756169247029noreply@blogger.comtag:blogger.com,1999:blog-36768584.post-83351942125709744332017-06-15T10:05:53.350-04:002017-06-15T10:05:53.350-04:00Jonathan:
Thanks! What cost per plasmid would te...Jonathan:<br /><br />Thanks! What cost per plasmid would tempt you to switch from Sanger? <br /><br />I'm guessing there isn't a cheap enough technology to best Sanger for your application, but useful to know the exact parameters.Keith Robisonhttps://www.blogger.com/profile/04765318239070312590noreply@blogger.comtag:blogger.com,1999:blog-36768584.post-54031324537750769882017-06-15T09:25:32.388-04:002017-06-15T09:25:32.388-04:00In my view Sanger sequencing serves a very differe...In my view Sanger sequencing serves a very different purpose than new sequencing technologies for at least my big chunk of the research field. I don't even think of our Illumina/PacBio work as being simlar to anything we do with Sanger, although they are all sequencing. We spend a lot of time constructing many smallish plasmids for essentially everything our genetics lab does, but we will make these sporadically, 1-2 this week, 5-6 the week after that, maybe 50 in one day next month. Any time these get made we need to verify that they were constructed correctly, and this can be done sufficiently with 2-3 Sanger runs per plasmid. I'm also spoiled by three different commercial companies with daily dropboxes with next-day service less than 200 feet from my lab. <br /><br />I'd love to know if there were any newer technologies remotely competitive with this (or the ABI 3730 downstairs). It would be nice to regularly get back full plasmid sequences instead of just our area of interest, but doing a library prep on individual plasmids even using the most economic methods I can find is already twice the cost of our Sanger runs, not including paying someone to sequence them and waiting for that to actually happen, unless we were doing dozens all at once in which case manually setting up a whole plate of Sanger reactions becomes worthwhile and even cheaper.<br /><br />Are there any newer technologies/services that let you get back sequences of small numbers of small plasmids or fragments economically and in a reasonable timescale?Jonathannoreply@blogger.com