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User Group Meeting

User Group Meeting. Software. Software Road Map. V2 Large Genome data collection and analysis – Done Lambda, AGP/FASTA Exports, and 2 color basic – Releasing Structural Variation and Haplotype Scaffolding and Consed integration Richer Information display and controls

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User Group Meeting

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  1. User Group Meeting Software

  2. Software Road Map • V2 Large Genome data collection and analysis – Done • Lambda, AGP/FASTA Exports, and 2 color basic – Releasing • Structural Variation and Haplotype • Scaffolding and Consed integration • Richer Information display and controls • Interactivity with data (merging, flipping, splitting, editing) • 2 Color full support

  3. Features: Recently Released • Reducing Irys scan time by optimizing scan controls • Cycle By Cycle exporting and processing workflow • Cluster processing through Sun Grid Engine support • Import BNX file and support other hybrid workflows • “Run” merging is 5x faster for large genomes • Statistics generation is 5x faster for molecule and labels • Loading of whole human genome is 5x faster • IrysView “Run” tab information redesigned • BNX file creation from Autodetect (V1.0 BNX) • Redesigned/convenient de novo Arguments selection

  4. Features: Soon to be Released (~3 weeks) • Rehydrate flow cell during run • Cleaning Module after each run • Lambda stretch variation compensation • AGP and FASTA export from IrysView • IrysView Marquee/Rubber band zooming in Browser • Run tab: run images and run data graphs • Merging: Lower memory and 2x faster

  5. Features: Currently in Development • Irys Sample detection • Rehydrate when indicated by sample detect • Improved find focus with encoder • Consed integration • Improved image processing • Diploid identification and visualization • Deeper structural variation integration • Show unaligned molecules and maps • Reference, Query, Molecule view • …and items that are discuss at the UGM

  6. Acknowledgements for Support and Feature Inspiration • Autodetect image processing: Angel and Yvonne (UCSF) • AGP file export: Jennifer (KSU) and Stefan (VIB) • Optional SGE to schedule and distribute jobs across multiple remote processes: Brian and Scott (NYGC) • 5x faster Statistics generation for molecule and labels: Jennifer (KSU) • 5x faster merging of large datasets and V2 chip human data: Many (KSU, Genergy, NYGC) • Rubber Band/ Marque zoom in browser : Many (Field Support) • Double click on viewer to center any map region: Ernest (BNG) • Remember Pen size and Coverage between xmaps and irysView sessions: Many (Field Support) • More convenient access to snipping tool: Denghong (BNG) • Import BNX into workspace: many (Field Support) • FASTA Exporting: many (Field Support)

  7. User Group: Software Tracks

  8. The 4 Step Basic Irys/IrysView Workflow Track 4 – Workflow by File Formats 3rd Party irys AutoDetect irysView Track 1 - Simulator Track 2 - Operation *repeated in Sample Tracks Track 3 - Visualization Bonus Track – Everything else • Hands-on Irys Simulator • The basics of navigating the Irys screens • Hands-on IrysView Operation • The basics of loading Irys results, running analysis tools, and visualizing • Hands-on IrysView Visualization • Detailed control and operation of the browser to find and investigate features • Hands on File Formats in the Irys/IrysView Workflow • A review of the workflow from the perspective of the files, the content and the formats to support the workflow

  9. Track 1 - Hands-on Irys Simulator • Purpose • A quick method of walking through the software operation of Irys without having to wait for instrument responses • This will also be presented in the Sample Prep Tracks • Agenda • Startup • Load chip • Focus • Registration • Select recipe • Scan chip • Rehydrate • Finish run • Wash • Shutdown

  10. Track 2 - Hands-on IrysView Operation • Purpose • A introduction or quick review to the operation of IrysView • Agenda • Load a data set from the network • Refresh a data set to get more cycles • Show a run report • Change SNR and molecule filter • Show the graphs for the run stats • Merge some data sets • Configure and start a de novo assembly • Look at the molecule mapping to the assembly in the browser • Run a map report • Run an assembly report • Load some references • Import a BNX • Compare an assembly to a reference • Show the XMAP browser and chromosome navigation

  11. Track 3 - Hands-on IrysView Visualization • Purpose • A detailed dive into the control and operation of the IrysView browsers to identify interesting genomic features • Agenda • Reviewing Run Images, Run Graphs, and Run Reports • De novo assembly control • Reviewing Molecule mapping to Consensus map • Viewing Reference and Query Genome Browser

  12. Track 4 - Hands on File Formats in the Irys Workflow • Purpose • Understand how the workflow generates files and the information that they contain • Agenda • Irys: Generates TIFFs, metadata.xml, autofocus.csv, • AutoDetect: Reads TIFF and create MOL, LAB, BNX • IrysView: Reads BNX and filter BNX • IrysView de novo runs Refaligner and Assembler • Read BNX and generate CMAP, SMAP, AMAP • IrysView comparison: Reads 2 CMAP and creates XMAP • Bonus: Create BED files created from SMAP

  13. Track Bonus – Everything Else • Purpose • Handle anything software not covered by the tracks • Agenda • Cluster Processing • Your specific situation / request / issue • Where • Find Kirt

  14. Software and Data AnalysisTracks: Pick 2 SW Bonus track – anything else SW – See Kirt

  15. Schedule of Tracks SW Bonus track – anything else SW – See Kirt

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