1. Click to edit Master title style User Group Meeting Software

2. Software Road Map 1.V2 Large Genome data collection and analysis – Done 2.Lambda, AGP/FASTA Exports, and 2 color basic – Releasing 3.Structural Variation and Haplotype 4.Scaffolding and Consed integration 5.Richer Information display and controls 6.Interactivity with data (merging, flipping, splitting, editing) 7.2 Color full support 2

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 3

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 4

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 5

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) 6

7. User Group: Software Tracks 7

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

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 9

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 10

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 11

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 12

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 13

14. Software and Data Analysis Tracks: Pick 2 14 TrackTitleDescriptionLocation 1Irys SimulatorSimulate Irys operation on the desktop for navigation and orientation Analysis Station One 2IrysView Overview Walk through importing a run, reviewing stats and reports, de novo assembly, and comparison to reference Analysis Station Two 3IrysView Visualization Using a human data set, show how to navigate and control the browser to find and display interesting information Analysis Station Three 4File Formats and Workflow Show example file formats (BNX, CMAP, XMAP, SMAP, AMAP) and where they are created and consumed in the workflow Analysis Station Four 5 De Novo CMD Line Executing a genomic assembly on the command line Ribosome 6 De Novo IrysView Using IrysView to control assembly and alignmentNucleus 7 Structural Variation Structural variation detectionAnalysis Station Five SW Bonus track – anything else SW – See Kirt

15. Schedule of Tracks 15 User Group Meeting Jan 10, 2014 Morning Group - Analysis Afternoon Group - Analysis Track Name Session Leader(s) 9:30 to 10:0010:00 to 10:4510:45 to 11:30 1:00 to 1:301:45 to 2:302:30 to 3:00 # 30 min45 min 30 min45 min 1 Irys Simulator Chris & James Intro by Alex and Kirt Irys in Lab Intro by Alex and Kirt Irys in Lab 2 IrysView Overview Andrew & Michael Irysview Overview 3 IrysView Visualization and File FormatsThi Browser 4 File Formats & WorkflowVuFile Formats 5 de novo cmd line Heng & Ernest de novo cmd 6 de novo IrysViewAlex de novo IrysView 7 Structurial Variation Warren & Andy Structurial Variation SW Bonus track – anything else SW – See Kirt