Bionano Access v1.2 Release Notes

Table of Contents Bionano Access... 3 Updates... 3 Bionano Access... 3 Introduction... 3 Compatibility... 3 Note: BNX Merge... 4 Improvements... 4 Tickets... 11 Technical Assistance... 14 Page 2 of 14 30220 Rev A, Bionano Access v1.2 Release Notes

Bionano Access Revision Revision A Notes Initial release of document. Updates The following updates have been made to the 1.2 release of Bionano Access. Update Change Ticket 1.2.1 MQR does not start for merged BNX IW-3223 Mol to Maps view blank if multiple tabs open IW-3221 CPMR region does not extend to end of map IW-3164 Reset user colors to default IW-3170 Dashboard row span incorrect IW-3174 Incorrect Assemblies listed for 2 Enzyme Hybrid Scaffold IW-3177 Total Chip DNA incorrect on dashboard IW-3180 Bionano Access This document describes the v1.2 release of Bionano Access TM. In this document we will provide an overview of what is changing with this release so that you may better understand the impact of moving to this version of our visualization software. Should you have any questions please contact support@bionanogenomics.com. Introduction Bionano Access v1.2 is a new release of our Bionano Access product. Bionano Access v1.2 supports Windows, Mac, and Linux systems. Data between users is shared using projects, and performance is much improved through rendering optimizations and graphics acceleration. This application is designed for install on a single centralized server that can be shared across an organization. For information about system requirements and installation please refer to our Installation Guide (P/N 30170). Compatibility Bionano Access is compatible with data generated on both Irys and Saphyr instruments. Existing Irys Data generated via Auto Detect v2.1.4 or IrysSolve v2.1 pipeline can be uploaded into Bionano Access. Bionano access is compatible with Saphyr Control Software versions 3.0 and 3.1. Bionano Access is designed to integrate directly with the Bionano Solve TM v3.2.1 pipeline running on the IrysSolve, Saphyr Compute and Bionano Compute servers and many custom clusters running SGE for scheduling (see the Installation Guide, part number 30170 for the configuration details). Compute configurations which are not directly compatible will continue to be supported from the command line, with a manual import of results into Bionano Access. 30220 Rev A, Bionano Access v1.2 Release Notes Page 3 of 14

Note: BNX Merge When merging BNX files it is important to only merge files of consistent quality and related content. BNX files generated by Bionano Access 1.2 and Bionano Tools 1.2 cannot be merged with BNX files generated in previous versions. However, hybrid scaffolding can be performed on BNX files coming from Bionano Access 1.1 and 1.2 using the two enzyme workflow. Please consider this when deciding to upgrade your system. Improvements Improvement New copy number algorithm Description There is a new copy number algorithm in Bionano Solve 3.2 (See P/N 30210Intro to Copy Number Analysis for more details). Bionano Access includes improved visualization to display this new output. To see the copy number track, turn on the show copy numbers option in the view options dialog. The system will display a smoothed line with highlighted regions for gains and losses. As you zoom in, the system will begin to show the individual copy number values for each label. The new copy number data will only be available on assemblies generated using Bionano Solve 3.2. Copy number smooth line: Label copy number values (zoomed in from image above): Page 4 of 14 30220 Rev A, Bionano Access v1.2 Release Notes

Filter SV by Type It is now possible to apply different confidence filters based on the type of SV. Click the SV Confidence link on the viewer toolbar to access the filter dialog. SV Confidence link on the toolbar: SV Confidence Filter Dialog: Filter by SV Size New Match Columns CPMR visualization SV size column has been added to the SV Tab in the viewer to facilitate filtering SVs by size. The following columns have been added to the Match tab in the viewer: Ref Contig ID, Ref Start Pos, Ref End Pos, Orientation, and Confidence. The system now tracks if a label is in a complex multi-path region (CMPR). CMPR regions are those where maps cannot fully resolve the correct paths (due to segdups, large inversions, etc ) This information appears in the tooltip when you hover over a label. The viewer in Bionano Access 1.2 will also highlight CMPR regions as shown below. You can change the color of CMPR regions in the viewer options dialog. CPMR Region example: Align Reference When performing an alignment operation, the user now has the ability to select existing references in the system. 30220 Rev A, Bionano Access v1.2 Release Notes Page 5 of 14

Alignment multiple contigs Pre-Assembly In previous versions of Bionano Access the viewer only displayed the first alignment in the results. Now if there are multiple alignments the user can access all of them. The Pre-Assembly option adds steps to the de novo assembly process to help with samples that have no reference or if their reference is poor. This option will be turned on automatically if the sample has no reference. If you have a reference you will have the option enable Pre-Assembly. It will be turned on by default if your sample is not human. Page 6 of 14 30220 Rev A, Bionano Access v1.2 Release Notes

New De Novo Assembly Dialog The number of de novo assembly opt arg config files in Bionano Solve 3.2 increased significantly to support new settings for DLS, large genomes, extend and split, CMPR cutting, and more. To help the user select the correct configuration, the de novo assembly dialog has been modified. The user can now respond to a few prompts and the system will automatically determine the correct configuration to use. If the user prefers to select the configuration file to be used manually or create their own custom configuration they can choose to use a custom configuration (set Use Custom Config to Yes) and the list of configuration files will be displayed. New de novo assembly dialog: De novo assembly dialog when using a custom configuration: Dashboard Changes The scale on the dashboard graphs will switch from cohorts to scans after one full scan has been captured. The dashboard now shows the total data captured on the chip which is helpful if you have performed more than one run using the same chip. The reference name has been added to the prep column so you know what reference was used to generate the map metrics. 30220 Rev A, Bionano Access v1.2 Release Notes Page 7 of 14

DLS Support SCP Image Detection Database Performance Improvements Reference Enzyme Selections To support DLS samples, we have added new references, new configuration files,, new cluster configurations, and new operations. Bionano Access will now transfer files to and from compute resources using SCP. This alleviates the need to mount and export drives between the systems. This also allows different drive systems for each compute cluster and it eliminates UID issues. The Bionano Access image detection process has been accelerated by 30% by optimizing database queries and caching query results that are reused during a chip run. In previous versions when you added a Reference, you were prompted for the enzyme motif. Enzyme motifs can be hard to remember. Now you can select the enzyme from a list of enzymes already known in the system. You can also click the Add Enzyme button to add a new enzyme if needed. You can select more than one enzyme in the list if needed. Bulk Object Delete When objects are deleted in the Project Browser they go into the trash. Administrators can permanently delete objects in the trash. There is now a button to allow Administrators to delete all the objects in the trash so they don t have to delete them one at a time. Page 8 of 14 30220 Rev A, Bionano Access v1.2 Release Notes

Genome Map Alignment The default alignment for consensus maps has changed. Previously, Access would align the maps left to right. Now Access aligns first to the highest confidence match group. As a result, match lines tend to be more vertical and straight. This is a fairly subtle example, but you can see the lower maps in this case are not inverted. Before: After: No Molecules If there are no molecule alignments associated with a map in the viewer the Show Molecules option in the right click menu will no longer be available. 30220 Rev A, Bionano Access v1.2 Release Notes Page 9 of 14

Label Z-Fighting When zoomed out in the viewer, there are typically enough labels that they will visually overlap. Each enzyme has a matched color and an unmatched color designated. The graphics library did not choose which color to display in a balanced way when different label colors overlapped. It tended to favor darker colors which typically corresponded to our unmatched label colors. Since matched enzymes typically far outnumber unmatched labels, the z-level of the matched labels is changed so the matched color will be favored when different label colors overlap. As a result, many maps now turn a solid color for the matched labels. Unmatched labels that are under matched labels will appear as you zoom in. Here is a section of one DLE-1 example. In this case, light purple is the matched color and black is the unmatched color. Before: After: In Silico Digestion One Step MQR Cancelled Previously when starting In Silico Digestion, you had to upload the FASTA file first and then subsequently launch the digestion. The system now does both actions in one single step. Bionano Access automatically cancels jobs that are active for more than 10 days. Jobs that are active for longer than 10 days are assumed to have been interrupted or orphaned. If the user started an MQR job on a molecules object that was created over 10 days ago, the job was being cancelled automatically by the system. The create date is reset for new MQR jobs now so they do not get cancelled. Page 10 of 14 30220 Rev A, Bionano Access v1.2 Release Notes

NCBI Export Status Change When an NCBI export starts, the first step is to zip the NCBI Export files for download. There was no visual indicator to let the user know the file zip was in progress, so it seemed like nothing was happening. Due to the size of the files being compressed, the step to zip files could longer than one minute. Now the user will get a message to let them know the files are being compressed and packaged for download so they understand their operation is in progress. Tickets User Stories Summary Ticket [3 Level] Add copy number variation tab in viewer IW-1866 [3 Level] Add default filter for each SV Type IW-2945 [3 Level] Filter by SV size IW-190 [3 Level] Hide copy number segments on active filter IW-2981 [3 Level] Include additional alignment information in match table IW-2897 [3 Level] SV Type Confidence Filter IW-2886 [3 Level] Visualization for segmental duplications IW-3023 [Alignment] Ability to use reference in alignment IW-2688 [Alignment] Handle alignments with more than one contig IW-2600 [Assembly] Add Pre-Assembly option IW-2761 [Assembly] Add prompt for cutting segmental duplications IW-3022 [Assembly] Simplify generate de novo assembly dialog IW-2946 [Assembly] Support New Opt Args IW-3047 [Copy Number] Per label copy number IW-1841 [Dashboard] Include reference name IW-2674 [Dashboard] Omit failed map metrics IW-2776 [DLS] Add DLE-1 References IW-2680 [Exp Design] Plot Metrics by Scan IW-2556 [Help] Show current versions on help screen IW-2762 [MQR] New fields from Access IW-2970 [Project Browser] Show command line instead of job details IW-2899 [Project Browser] Use object alias for object download file name IW-1969 [Project Browser] Bulk object delete IW-1572 [Pronto] Cache Run Data IW-2654 [Pronto] Eliminate Dependency on Curl IW-1847 [Pronto] Improve Query Performance IW-2653 [Pronto] Switch to SCP IW-2795 [Reference] Bulk delete IW-623 [Reference] Enzyme Sequences not known IW-1922 [References] Add hg38 references IW-2679 [Scaffold] Can't select Molecules for assemble object IW-1247 30220 Rev A, Bionano Access v1.2 Release Notes Page 11 of 14

Defects Summary Ticket [3 Level] Bed file disappears when switching chromosomes IW-3014 [3 Level] Cannot find correct contig in Two Enzyme Hyrbrid Scaffold IW-1754 [3 Level] Cannot handle four alignment objects at once IW-2824 [3 Level] Cannot hide labels in Ref to Mol alignment IW-3071 [3 Level] Change default map alignment IW-2887 [3 level] Crash when loading bed file IW-3021 [3 Level] Hide show molecules option IW-3059 [3 Level] Invert map does not invert molecules IW-2735 [3 Level] Label color z-fighting IW-2772 [3 Level] Labels not displaying in molecules to maps alignment IW-2534 [3 Level] Molecules backbone not showed when in stretched mode IW-2591 [3 Level] Multiple alignments to single hybrid causes label errors IW-2930 [3 Level] Right click molecule pileup shows context menu IW-3082 [3 Level] Scaffold cut left-right should be paired not crossed IW-2780 [3 Level] Scaffold orientation changes when zooming IW-2598 [3 Level] Selected labels are not highlighted IW-3067 [3 Level] Show molecule match lines viewer option not functional IW-3091 [3 Level] SVG image save fail for workflow IW-3068 [3 Level] Viewer reloads when changing resolution IW-2933 [Alignment] System tries to read file name for contig id IW-2705 [Assembly] Reference names out of order IW-2750 [Bnx Workflow] Add population index to molecules object name IW-2898 [Bnx Workflow] ChipStatus returning bp instead of Gbp IW-2963 [Bnx Workflow] getversions API locks up Access IW-2893 [Bnx Workflow] image path not updated on chip resubmit IW-2753 [Bnx Workflow] MergeRun job cancelled IW-2857 [Dashboard] Add chip stats to dashboard IW-2995 [Dashboard] End time appears after one FC is complete instead of both IW-2660 [DLS] Add DLE-1 Mask Bed file IW-2849 [Exp Design] Too many chips block Done button on confirmation screen IW-2854 [Help] Video controls hidden in safari IW-2642 [Knickers] upload and launch not one step IW-2699 [MQR] Dual labeled sample MQR hard to read IW-2480 [MQR] Job automatically cancelled IW-2721 [MQR] Missing Label Density IW-2693 [Project Browser] NCBI export is slow to respond IW-2647 [Project Browser] Permanent delete list does not auto refresh IW-2989 [Project Browser] Prevent quotes in object alias IW-2931 [Project Browser] Remove dialog X when processing IW-2844 [Project Browser] Remove object does not auto select first row in list IW-2997 [Project Browser] Reports MQR success despite active job IW-2837 [Project Browser] Sort by newest created date first IW-2626 Page 12 of 14 30220 Rev A, Bionano Access v1.2 Release Notes

[Project Browser] Update scaffold opt argument files for 1.2 [Project Browser] Job listing window columns not resizable [Reference] Configuration Edit Window not Refreshed [Reference] Duplicate enzyme sequence not added [References] Bulk delete does not refresh list [References] Deleting reference removes related molecule object from database [References] hg38 file name has typo [References] Reference list not in order [Safari] Apple Safari can't see colors in settings nor change colors [Safari] Map locked with mouse when I right-clicked a track [Safari] Rule on Reference Map disappears [Scaffold] Status is not updated [Scaffold] Optimize import [SV Merge] Cancelled VAP can start SV Merge [Variant] Add duplication parameter IW-3060 IW-2081 IW-2788 IW-3031 IW-2926 IW-2986 IW-2950 IW-2754 IW-2513 IW-2935 IW-2934 IW-2632 IW-2751 IW-2910 IW-3056 30220 Rev A, Bionano Access v1.2 Release Notes Page 13 of 14

Technical Assistance For technical assistance, contact Bionano Genomics Technical Support. You can retrieve documentation on Bionano products, Safety Data Sheets, certificates of analysis, frequently asked questions, and other related documents from the Support page or by request through e-mail and telephone. Type Email Phone Contact support@bionanogenomics.com Hours of Operation: Monday through Friday, 9:00 a.m. to 5:00 p.m., PST US: +1 (858) 888-7600 Website www.bionanongenomics.com/support Page 14 of 14 30220 Rev A, Bionano Access v1.2 Release Notes