Korlach: Human de novo assemblies - from HuRef and six others - 3.25Gb total assy size for PacBio (since the N50's are ~4.5k) #AGBT14
2:43pm February 14th 2014 via Hootsuite
Korlach: 2d ago released 54x long-read coverage de novo PacBio assembly Press Release: http://t.co/n27XN2Tt3e #AGBT14
2:42pm February 14th 2014 via Hootsuite
Next up: Pacific Biosciences, Jonas Korlach: No Assembly Required: Extremely Long Reads for Full-length Transcript Isoform Seq #AGBT14
2:40pm February 14th 2014 via Hootsuite
Ohgami: Looked at mut type against AML subtype (of 4); survival and U2AF1 mutation; retrospective samples several mis-classified #AGBT14
2:37pm February 14th 2014 via Hootsuite
Ohgami: 77 AML samples, went through HaloPlex Molecular Inversion Probe method, sequenced on MiSeq and used SureCall s/w #AGBT14
2:34pm February 14th 2014 via Hootsuite
Ohgami: A well-defined genomic world for myeloid neoplasms (genes and pathways). Chose ~20 genes + 2000x coverage + HaloPlex #AGBT14
2:33pm February 14th 2014 via Hootsuite
Ohgami: But for hematologic neoplasms: classification involves many factors; now molecular data is much more prominent #AGBT14
2:31pm February 14th 2014 via Hootsuite
Ohgami: 'Targeted NGS of AML in Clinical Research'. Speakers background is pathology. Majority of cancers are carcinomas. #AGBT14
2:29pm February 14th 2014 via Hootsuite
Yi: SureCall software, free of charge, both HaloPlex and SureSelect, both exomes and custom. http://t.co/ARMXmwEqSM #AGBT14
2:26pm February 14th 2014 via Hootsuite
Yi: Transposase-based, 90min hyb. "<7h, 30m hands-on time, no fragmentation equipment req'd Better performance than 'competitor I' #AGBT1
2:24pm February 14th 2014 via Hootsuite
Yi: Preview of a new product: SureSelect^QXT - sample-to-seq in 1 day; 3x faster and 50ng input. Exomes & custom #AGBT14
2:23pm February 14th 2014 via Hootsuite
Up next: Yong Yi (Agilent Technologies) and Bob Ohgami (Stanford) New Agilent NGS Products – Advances in NGS Clinical Research #AGBT14
2:21pm February 14th 2014 via Hootsuite
Bready: Q: (Grills) Throughput? A: Data is immediate, 8 indep. on-deck; typically about 1h/sample #AGBT14
2:19pm February 14th 2014 via Hootsuite
Bready: Q: Any work with PacBio users (for long molecule sample prep)? A: Yes, but can't comment. #AGBT14
Bready: Q: Presumably not working on FFPE? A: Primarily focused on long molecules. Liquid tumors, not focus now. #AGBT14
2:18pm February 14th 2014 via Hootsuite
Bready:Looking at a cytogenetic application (FISH, karyotyping, aCGH): dense chart shows (?) much better resolution #AGBT14
2:16pm February 14th 2014 via Hootsuite
Bready: Nabsys maps can correct assembly errors, and do de novo, working on 'push-button de novo' combining NGS short-reads #AGBT14
2:15pm February 14th 2014 via Hootsuite
Bready: Illustrating a E. coli phylogenetic tree, and similarity between different strains (BL21, K-12 etc.) maps are dissimilar #AGBT14
2:13pm February 14th 2014 via Hootsuite
Bready: Workflow includes DNA extraction, probe attach, incubate with NPS reagent, load, analyze. #AGBT14
2:11pm February 14th 2014 via Hootsuite
Bready: Doing de novo assembly, simply lining up the tags. Instrument has 8 modules, independent of each other #AGBT14
2:10pm February 14th 2014 via Hootsuite
Bready: Showing deletion, translocation, inversion and how the maps would clearly & easily distinguish them #AGBT14
2:09pm February 14th 2014 via Hootsuite
Bready: Pressure- and voltage-based control; molecules of all sizes. 150ms traces - 150K bp, ~26 tags detected across the 150kb #AGBT14
Bready: Looks like a huge funnel at top, pass thru a single point, and then expand outward after the detection point #AGBT14
2:08pm February 14th 2014 via Hootsuite
Bready: Electronic data collection at high resolution, and long lengths. Electron micrograph of the detector #AGBT14
2:07pm February 14th 2014 via Hootsuite
Bready: Their readlength - ~100KB - sequence-spec tags, driven through a single detector at high velocity, 1MB/sec #AGBT14
2:06pm February 14th 2014 via Hootsuite
Bready: Long-range mapping tech: electronic has no diffraction limit like light has, much higher resolution #AGBT14
Bready: Illustrates their mapping ability as knowing the box picture for a puzzle; the 'big picture' that includes structural info #AGBT14
2:03pm February 14th 2014 via Hootsuite
First up: Barrett Bready (Nabsys) Correcting Genome Assemblies Using Semiconductor-Based, Single Molecule Genomic Mapping #AGBT14
2:02pm February 14th 2014 via Hootsuite
Myers: Q: Dazzler release? A: Only when it's ready, extract tool soon, but correction needs some more work (to make it easier). 1mo #AGBT14
12:08pm February 14th 2014 via Hootsuite
Myers: Q: Will you look at transcriptome assemblies? A: A hybrid strategy would be a good thing. May not have enough PacBio copies #AGBT14
12:07pm February 14th 2014 via Hootsuite
Myers: LR enables de novo, reference quality reconstructions, great for comparative genomics, and large scale variation #AGBT14
12:06pm February 14th 2014 via Hootsuite
Myers: Concl: high error 'is not a quality issue' - only efficiency and consensus. Eff problem solved here. #AGBT14
Myers: 2TB to 150GB filesizes using .dexta with PacBio human data #AGBT14
12:05pm February 14th 2014 via Hootsuite
Myers: G.bax.h5 'is a moose' of a file; fasta to .dexta down to 1/14th the size. #AGBT14
12:04pm February 14th 2014 via Hootsuite
Myers: Can correction be bypassed? A hard question. All pure strategies - PacBio only, then assemble. #AGBT14
12:03pm February 14th 2014 via Hootsuite
Myers:50x human, 512 cores, 5 days to assemble in 16GB. Uses DFS, will take 100x longer if not. #AGBT14
12:02pm February 14th 2014 via Hootsuite
Myers: Only FASTAs needed for input, quality comes in after for consensus for Quiver. Shows E.coli, Arabidopsis, Human assy times #AGBT14
Myers: 36x faster - Dazzle vs. Blaser, more sens, catches same true positives. Overlap, scrub, correct, overlap, scrub, assemble #AGBT14
12:00pm February 14th 2014 via Hootsuite
Myers: You don't know when the PacBio error spikes (technology problem) but after consensus correction, to 0.5% error rate at 10x #AGBT14
11:59am February 14th 2014 via Hootsuite
Myers: Don't think about the graph; scrub the underlying data. "This is for the gear-heads". (Comment: great talk nonetheless) #AGBT14
11:57am February 14th 2014 via Hootsuite
Myers: Illustrates a string graph problem - contiguous stretches of underlying genome (untrue with real-world data), and error rate #AGBT14
11:56am February 14th 2014 via Hootsuite
Myers: String graphs are the real problem. His paper from 2005 http://t.co/h4tlst8Fn0 #AGBT14
11:54am February 14th 2014 via Hootsuite
Myers: 20x of 15% data gives Q70; the problem is the ability to assemble efficiently. Punch-line: 'We're 37x faster" on a modest h/w #AGBT14
11:53am February 14th 2014 via Hootsuite
Myers: At perfect Poisson, would get 100% coverage; 'this is why I'm excited' with PacBio data #AGBT14
11:52am February 14th 2014 via Hootsuite
Myers: Implications - the higher x, the accuracy will converge geometrically with depth. #AGBT14
Myers: Talking about RS 2 - P4/C2, 11% insertion, 3% deletion, 1% subst. But errors are random; read sampling also >nearly< random #AG
11:51am February 14th 2014 via Hootsuite
Myers: After a 10y hiatus, knew short-reads were not 'intellectually satisfying to me' (in the meantime) #AGBT14
11:50am February 14th 2014 via Hootsuite
Gene Myers, Max Planck Institute for Molecular Cell Biology and Genetics: A de novo Whole Genome Shotgun Assembler for Noisy LR Data #AGBT
11:49am February 14th 2014 via Hootsuite
McCombie: Q: What about >7.5kb cutoff? A: Not that many really long reads; need new isolation procedures to get unbroken DNAs #AGBT14
11:48am February 14th 2014 via Hootsuite
McCombie: Q: (Mardis) At 100x, is it purifying selection? A: 100x total coverage, >10kb reads a lot lower at 20x or so #AGBT14
11:47am February 14th 2014 via Hootsuite
