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Agbt 2013 final
- 1. INCREASED READ LENGTHAND IMPROVED GENOMEASSEMBLIES WITH PACIFIC BIOSCIENCES XL DNA POLYMERASE Antoniou E., Schatz M., Koren S., Rank D. ,Peluso P. , MoCombe P., Khitrov G. , McCouch S., McCombie R.
- 2. Product Releases Since Last AGBT Feb 2012 C2 Launch May 2012 v1.3.1 SW Release – Base Mods Aug 2012 v1.3.2 MagBead Release Nov 2012 v1.3.3 – Stage Start, XL Chem Jan 2013 SMRT Cells V3
- 3. 40 tons of duckweed per acre per year ~.1 tons per day not accounting for seasonal affects .1 ton of duckweed yields ~ .025 tons of ethanol by weight and is ~7.5 gallons/day Duckweed – the new Biofuel ? Rob Martienssen, Evan Ernst Can duckweed save the world from global warming? by Rich Bowden - Apr 9 2009 - www.thetechherald.com
- 4. Duckweed C2 versus XL performances; 1 XL C2 N50 bases = 3863 N50 bases = 5035
- 5. Duckweed C2 versus XL performances; 2 C2 XL
- 6. Duckweed C2 versus XL performances; 3
- 7. Macrostomum lignano a free-living flatworm with high regeneration capacity Greg Hannon, Kaja Wasik, Michael Schatz James Gurtowski Culture in laboratory easy; feed on diatoms; kept in Petri dishes with algae and light Transparency highly transparent Generation time 18 days Accessibility to eggs single eggs, whole year through Morphological knowledge well established Plasticity high; can endure extreme starvation Regeneration potential head regenerates posterior end with gonads; posterior end makes no new head Stem Cell System pluripotent BrdU/H3 Staining easy by soaking RNA interference easy by soaking Amenable to forward and reverse genetics yes Genome size and availability 700 MB, 5x coverage; early draft online http://www.macgenome.org/
- 8. Worm; Compare two librariesThe quality of the sequencing library matters Library 1 Library 2 N50 bases = 4640 N50 bases = 5122
- 9. Genome size is estimated at about 700 Mb All Paths Illumina; 40X coverage PacBio corrected reads; 7X The ALLPATHS assembly; 62MB The Celera assembly; 435M With only short reads (fragment and jump libraries) ALLPATHS gave us: 1.7kb N50 contig size 2kb N50 scaffold size 4kb N50 scaffold size with gaps With only error corrected Pacbio Reads, Celera gave us: 7kb N50 contig size Macrostomum lignano preliminary genome assembly
- 10. - more than 3.5 billion people depend on rice for more than 20% of their daily calories - About 90% of rice is grown in Asia - In Africa, rice is the fastest growing food staple - An additional 8-10 million tons of rice needs to be produced every year - The challenge is to produce this additional rice with less land, less water, and less labor, in more efficient, environmentally-friendly production systems that are more resilient to climate change Rice
- 11. Rice genome About 430 million base genome About 40% repeats High quality, BAC by BAC reference available Relatively easy to get high quality DNA Useful model for other cereal genomes
- 12. 0.35X bead clean up 0.45X bead clean up N50 bases = 3821 N50 bases = 4382
- 14. Assembly Contig NG50 Illumina Fragments 50x 2x100bp @ 180 3,925 MiSeq Fragments 23x 459bp 8x 2x251bp @ 450 6,332 “ALLPATHS-recipe” 50x 2x100bp @ 180 36x 2x50bp @ 2100 51x 2x50bp @ 4800 18,248 PBeCR Reads 7x @ 3500 ** MiSeq for correction 25,724 PBeCR + Illumina Shred 7x @ 3500 ** MiSeq for correction 5x @ 3000bp shred 36,127 Preliminary Rice Assemblies In collaboration with McCombie & Ware labs @ CSHL
- 15. Dick McCombie Patricia MoCombe Melissa Kramer Stephanie Muller Panchu Deshanpe Michael Schatz James Gurtowski Pacific Biosciences Suzanna Wang David Rank Paul Peluso Cheryl Heiner Susan McCouch (Cornell) Namrata (Moni) Singh Rob Martienssen Evan Ernst Greg Hannon Kaja Wasik
Editor's Notes
- What was the movie time for the C2 runs?
- Same read quality profile between C2 and XL
- G=370792118