tag:blogger.com,1999:blog-36768584.post2800188100150280811..comments2024-03-03T18:49:34.382-05:00Comments on Omics! Omics!: E.coli Outbreak GenomicsKeith Robisonhttp://www.blogger.com/profile/04765318239070312590noreply@blogger.comBlogger5125tag:blogger.com,1999:blog-36768584.post-48134028585701491832011-08-20T06:04:57.781-04:002011-08-20T06:04:57.781-04:00Keith, It is interesting to find your article and ...Keith, It is interesting to find your article and assess it retrospectively. You posted your article on June 15, 2011 and as you stated, almost everyone and everything (BGI, U. of Muenster, HPA, Ion Torrent, OpGen, Illumina, 454) had all generated and released data for the outbreak. We now know that PacBio has released their reads and from their ZMW single read deposit in GenBank (http://www.ncbi.nlm.nih.gov/sra/92212) it is clear that they started data collection on June 10th with 32 closed circular ZMW read runs and June 18th with 24 ZMW long subread runs (http://www.ncbi.nlm.nih.gov/sra/87502) for just the outbreak isolate (not including all the other E. coli they sequenced). They must have had the outbreak isolate before June 10th in order to grow the organism, isolate DNA, shear the DNA, and make the SMRT-bell library for the closed circular reads. Considering BGI obtained a DNA sample somewhere around May 30th (3 days before they released the sequence) and OpGen received an isolate around June 6th (2 days before they released the whole-genome map), it doesn’t sound like PacBio received the isolate as late as they publically stated…really have to read the reports and between the lines to get all the information and to make conclusions on which platform and technology provides the best solution.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-9859263566461641402011-06-16T22:35:35.588-04:002011-06-16T22:35:35.588-04:00I think it's a typo: Eric Schadt, CSO of PacBi...I think it's a typo: Eric Schadt, CSO of PacBio.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-74207729478315025872011-06-16T20:53:29.746-04:002011-06-16T20:53:29.746-04:00I'm confused by the remark "I haven't...I'm confused by the remark <i>"I haven't tried to calculate error rates. Yes, that's a huge omission, but the problem is I'm not a specialist in E.coli any more (and haven't been for a long time) and am not sure what to trust in the assemblies."</i><br /><br />Even a rather crappy assembly can provide very good estimates of error rates for individual reads. Trying to determine how good an assembly is may require knowledge of the organism, but error models for the reads only require an assembly that is substantially better than the reads.<br /><br />It sounds like you have some pretty good assemblies (454 and Illumina data), so getting error estimates for the Ion Torrent is just a matter of mapping the reads.<br /><br />One caveat: different mappers report statistics differently. An "unmappable" read for one mapper is a high-error rate read for another.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-44075540289611230242011-06-16T16:56:03.325-04:002011-06-16T16:56:03.325-04:00How can a talk by Eric Schmidt suggest that biosur...How can a talk by Eric Schmidt suggest that biosurveillance is important for PacBio? Is he affiliated with this company?Karolnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-7799572450042866402011-06-16T04:28:49.910-04:002011-06-16T04:28:49.910-04:00I think that this public analysis project is quite...I think that this public analysis project is quite important for European bioinformatics and for open science in general.Mikaelhttps://www.blogger.com/profile/04159973709377061958noreply@blogger.com