McCombie: Arabidopsis strain Ler-0 sequenced, also O. sativa.10kb mean RL, max 54kb (!) #AGBT14
11:44am February 14th 2014 via Hootsuite
McCombie: Also did S. pombe dg21, max RL 35.4kb, mean 5.17kb, 275x in 5 SMRTcells "huge difference in loading efficiency" for PacBio #AGBT14
11:39am February 14th 2014 via Hootsuite
McCombie: Rice genomes about 450MB, wanted to try using new PacBio chemistry (P5-C3), uses yeast W303 strain; only >10kb fx used #AGBT14
11:37am February 14th 2014 via Hootsuite
Up next: W.R. McCombie, Cold Spring Harbor Laboratory: A Near Perfect de novo Assembly of a Eukaryotic Genome Using >10KB Reads #AGBT14
11:34am February 14th 2014 via Hootsuite
Jaffe: Q: Cp to PacBio? A: "Hard-pressed to find a method to get to zero errors". Something to be said for size, cost, portability #AGBT14
11:33am February 14th 2014 via Hootsuite
Jaffe: Q: K-mer disambiguation had two poly-G's A: Doesn't make sense for long homopol's 'from the data I've seen' #AGBT14
11:32am February 14th 2014 via Hootsuite
Jaffe: Q: What if it doesn't get better? A: Not quite the right Q; a large % of the bases are right, do sth else in the lab. #AGBT14
11:31am February 14th 2014 via Hootsuite
Jaffe: Q:(Mardis) Misleading title? A: Assembly would have introduced "a bunch of errors", so we did something that was useful. #AGBT14
11:30am February 14th 2014 via Hootsuite
Jaffe: Path forward is to improve base calling, and to mix pore types. #AGBT14
11:29am February 14th 2014 via Hootsuite
Jaffe: Small device, 5kb median, 10kb tail, long perfect stretches common; 'error clumps' repeatedly at one loci #AGBT14
Jaffe: Resolving ambiguities with ONT data one long repeat and tandem repeat. #AGBT14
11:28am February 14th 2014 via Hootsuite
RT @neilhall_uk: OK so far we can see that this data is not going to replace PACBIO in the near future. #AGBT14
11:26am February 14th 2014 via Hootsuite
Jaffe: Alternate paths, score them, can resolve the graph. 13x for Scardovia, smaller 1+ MB genome. Showed short-read assy #AGBT14
11:25am February 14th 2014 via Hootsuite
Jaffe: Just combining datatypes - use 250b ILMN data, use DISCOVAR for assembly. Explains edge and node, illustrates reads laid over #AGBT14
11:24am February 14th 2014 via Hootsuite
Jaffe: Some consistent artifacts - missing T-base (5/6 E. coli reads with missing base.) Could improve the algorithm; mix pore-types #AGBT14
11:22am February 14th 2014 via Hootsuite
Jaffe: Lots of good k-mers - how to think of this datatype. Showed segment of Scardovia reads #AGBT14
Jaffe: 84% of 5+kb reads have at least 1 perf. 50-mer. 100% have at least 1 perf. 25-mer. "Perfect windows punctuated by artifacts" #AGBT14
11:21am February 14th 2014 via Hootsuite
Jaffe: Long tail - histogram went to 12kb, still reads out further. #AGBT14
11:20am February 14th 2014 via Hootsuite
Jaffe: E. coli (6x), Scardovia(13x), 5kb read-length. Mode - about 4.5kb. Measured bioanalyzer against readlengths and it matches #AGBT14
Jaffe: 1 cm2 rect array, 512 pores, speed thru pore configurable. 1 to 100 bases / sec. Data today is 25 bases / sec #AGBT14
11:19am February 14th 2014 via Hootsuite
Jaffe: A probabilistic assignment of the signal. Possible to get the wrong k-mer. Illustrated MinION device, Oreo (TM) shown for ref #AGBT14
11:18am February 14th 2014 via Hootsuite
Jaffe: Each horizontal event turned into a k-mer. Computational model is not trivial - a lookup of an approx table, not discrete. #AGBT14
11:17am February 14th 2014 via Hootsuite
Jaffe: has pA on Y, time in s on X; six-mers along x-axis shown ("CTGCTT" etc.) #AGBT14
11:16am February 14th 2014 via Hootsuite
Jaffe: Current across membrane, >1 base at a time; current a fn of several k-mer bases. Pore -> signal -> kmers -> bases. Raw da
Jaffe: Start with HMW DNA; 'tether' an adapter; illustrating ONT nanopore illustration. Ratchets bases on top of the nanopore #AGBT14
11:15am February 14th 2014 via Hootsuite
Jaffe: Deamer nanopore reference from 1999: http://t.co/CrSPIH090n #AGBT14
11:14am February 14th 2014 via Hootsuite
Jaffe: From 1996 reference: Nanopore "In principle". Will talk about ONT (Oxford Nanopore) #AGBT14
11:13am February 14th 2014 via Hootsuite
Up next: David Jaffe, Broad Institute of MIT and Harvard: Assembly of Bacterial Genomes Using Long Nanopore Reads #AGBT14
11:12am February 14th 2014 via Hootsuite
Schuster: Q: Cross-breed with Andean condor? A: No, it would create a 'genetic freak' #AGBT14
11:11am February 14th 2014 via Hootsuite
Schuster: Informed breeding reference Pac Symp Biocomput 2010 http://t.co/9dFJivqO29 #AGBT14
11:10am February 14th 2014 via Hootsuite
Schuster: Tasmanian devil effort ("informed breeding") now in-place at the SD Wild Animal Park condor breeding facility #AGBT14
11:06am February 14th 2014 via Hootsuite
Schuster: Now searching for the 'super condor' in museum specimens. Then re-insert the alleles to strengthen existing species #AGBT14
11:05am February 14th 2014 via Hootsuite
Schuster: First time parthenogenesis shown in birds. 1345 SNPs to look at maternal homozygous calls. 1.4% errors or misaligns #AGBT14
11:04am February 14th 2014 via Hootsuite
Schuster: Parthenogenesis - of 625 birds, 2 parthenotes were discovered ("no contribution of the father") 41 SNPs in CFTR #AGBT14
11:03am February 14th 2014 via Hootsuite
Schuster: The big question: what kind of diversity? mtDNA 'looks grim': only 4 haplogroups. #AGBT14
11:00am February 14th 2014 via Hootsuite
Schuster: Assy 2 to be released later this year, N50 68kb scaffolds. Illustrated Moleculo data length distribution (longest 27kb) #AGBT14
10:56am February 14th 2014 via Hootsuite
Schuster: Uses a combination for genome assy: MiSeq, stitched to make longer 454-style, HiSeq, Moleculo & 454 data #AGBT14
10:55am February 14th 2014 via Hootsuite
Up next: Stephan Schuster (Penn State): California Condor: Population Genomics and Informed Breeding Aid Species Conservation #AGBT14
10:54am February 14th 2014 via Hootsuite
Suzuki: Q:(Mardis) What's the time-factors involved? A: 1w to 2w is reasonable timeframe. #AGBT14
10:18am February 14th 2014 via Hootsuite
Re: DeRisi talk - no focus on speeding up library prep or seq, only 90m of bifx. IMHO 2 PGMs, 318 chip = 8M reads in ~7h, not o/n #AGBT14
10:16am February 14th 2014 via Hootsuite
Suzuki: From 116 samples, looking at genotype in both host / parasite and gene exp. in host / parasite #AGBT14
10:10am February 14th 2014 via Hootsuite
Suzuki: Plasmodium tags vs. human - both in vitro and experimental correlated well. 10% of reads were Pf (Plasmodium f.) #AGBT14
10:07am February 14th 2014 via Hootsuite
Suzuki: 'Interactive' Transcriptome analysis - parasites mixed with host human cells, able to monitor both human and plasmodium exp. #AGBT14
10:06am February 14th 2014 via Hootsuite
Suzuki: Unculturable, focused in on collab. with Manado Indonesia (Coelacanth captured there) #AGBT14
10:05am February 14th 2014 via Hootsuite
Up next: Yutaka Suzuki, University of Tokyo. Interactive Transcriptome Analysis of Malaria Patients #AGBT14
10:04am February 14th 2014 via Hootsuite
DeRisi: Q: Just bulk library prep and seq? A: If you know what's wanted, but unknown if virus, bact. Just total nucl. acid #AGBT14
10:03am February 14th 2014 via Hootsuite
DeRisi:Q:(Mardis): Any way to systematize this? A: Autoimmune test on rat brain slices, proteomics etc. Also seq 'everything - done' #AGBT14
10:01am February 14th 2014 via Hootsuite
DeRisi: Q:(Mardis) Any other poss. other than brain biopsy? A: Seq serum as well, no reads there. #AGBT14
10:00am February 14th 2014 via Hootsuite
DeRisi: So the regular Leptosp. test came back negative, and would have come back in 2w - hard to culture. #AGBT14
9:59am February 14th 2014 via Hootsuite
DeRisi: Further work - confirmed strain to Puerto Rico. But published CDC test for validated test is only 60% sensitive. #AGBT14
9:58am February 14th 2014 via Hootsuite
