Bionano Access® Software User Guide Document Number: 30142 Document Revision: M For Research Use Only. Not for use in diagnostic procedures. Copyright © 2020 Bionano Genomics Inc. All Rights Reserved For Research Use Only. Not for use in diagnostic procedures. Table of Contents Table of Contents .............................................................................................................. 2 Legal Notice ...................................................................................................................... 6 Revision History ................................................................................................................ 7 Introduction ...................................................................................................................... 8 Bionano Access Terms ....................................................................................................... 9 Login to Bionano Access .................................................................................................. 10 User Roles...................................................................................................................... 10 Login ............................................................................................................................. 10f Bionano Access Modules ................................................................................................ 10 Help ............................................................................................................................... 11 User Profile .................................................................................................................... 11 Message Center ............................................................................................................. 12 Alerts ............................................................................................................................. 12 Menu .............................................................................................................................. 12 Projects ........................................................................................................................... 13 Create Project ................................................................................................................ 13 Export Project ................................................................................................................ 13 Import Project ............................................................................................................... 14 Delete Project ................................................................................................................ 14 Edit Project .................................................................................................................... 15 Give Users Access to View Projects................................................................................ 15 Deleted Projects ............................................................................................................ 15 Objects ............................................................................................................................ 17 Menu .............................................................................................................................. 17 Objects List .................................................................................................................... 17 Object Details ................................................................................................................ 18 Object Options ............................................................................................................... 18 Alignment Options ........................................................................................................... 18 De Novo Assembly or Annotated De Novo Assembly Options ................................................. 18 Rare Variant Analysis or Annotated Rare Variant Analysis Options.......................................... 19 Variant Annotation Pipeline Options ................................................................................... 19 EnFocusTM FSHD Analysis Options ...................................................................................... 19 Bed Option ..................................................................................................................... 19 FASTA Option .................................................................................................................. 19 Map Options .................................................................................................................... 19 Molecules Options ............................................................................................................ 19 Scaffold Options .............................................................................................................. 20 Object Operations .......................................................................................................... 20 De Novo Assembly or Annotated De Novo Assembly Operations ............................................ 20 Rare Variant Analysis or Annotated Rare Variant Analysis Operations ..................................... 20 EnFocusTM FSHD Analysis Operations .................................................................................. 20 Map Operations ............................................................................................................... 20 Molecules Operations ....................................................................................................... 20 Import Object ................................................................................................................ 21 Import Molecules ............................................................................................................. 21 Import Consensus Map ..................................................................................................... 22 Import an Alignment Object .............................................................................................. 23 30142 Rev M, Bionano Access Software User Guide Page 2 of 86 For Research Use Only. Not for use in diagnostic procedures. Import FASTA ................................................................................................................. 24 Import Scaffold ............................................................................................................... 24 Import De Novo Assembly ................................................................................................ 25 Import BED ..................................................................................................................... 26 Import Cytoband ............................................................................................................. 27 Import Rare Variant Analysis ............................................................................................. 28 Import FSHD Analysis ...................................................................................................... 28 Import Variant Annotation ................................................................................................ 29 Remove Object .............................................................................................................. 30 Copy Object ................................................................................................................... 31 Edit Object ..................................................................................................................... 31 Jobs ............................................................................................................................... 32 Samples ......................................................................................................................... 32 Menu ............................................................................................................................. 32 Reset ............................................................................................................................. 33 Deleted Object ............................................................................................................... 33 Download Object ........................................................................................................... 34 Experiments .................................................................................................................... 35 Add Experiment ............................................................................................................. 35 Create an Experiment Template ..................................................................................... 38 Monitor Run Progress .................................................................................................... 38 Run Information .............................................................................................................. 39 Analysis Graphs ............................................................................................................... 39 Run Metrics Table ............................................................................................................ 40 Please refer to Bionano Access Dashboard Guidelines 30304 for more