If you are using our Starter plan, please refer to our Getting Started Guide for Starter Plan.
This guide aims at getting you up and running quickly with Geneious Biologics and includes the following topics:
- Adding users
- Workspace and Folders
- Folder sharing
- Importing and uploading files
- Analyzing NGS sequences with the Antibody annotator
- Analyzing Sanger Sequences
- Visualizing results
- Barcodes, UMIs, Single Cell Analysis and 10X
- Need more help?
More detailed articles can be found in this knowledge base, and several are directly linked within this guide. Step-by-step tutorials of common workflows can also be found here.
The Workflows and Flowcharts for Antibody Analysis page contains visual representations of the paths through Geneious Biologics from pre-processing to analysis and beyond. The flowcharts also provide guidance on how to analyse various kinds of sequences - Sanger, NGS and NGS with UMIs and/or Barcodes (Single Cell Analysis).
When you start with Geneious Biologics, you will receive an email from Geneious with an account activation link. Simply follow that link to set up your password. For more detail about account set up and trouble shooting tips, see here.
Important: Google Chrome is the browser we test with and officially support. We suggest you use the latest version of Chrome so you will always get the best experience. Some of our users also use Microsoft Edge Chromium.
Adding users (Admin only)
To add a new user into your organisation, click Users in the sidebar and click New in the main page. Only administrators can manage users.
Fill in the appropriate details and click Create User.
A Geneious account activation email will be sent to the email address which contains instructions on password setup and account activation.
For more information about users and user groups, see here.
Workspace and Folders
Folders (folder icon in the folder tree) may contain any mixture of documents, such as nucleotide sequences, protein sequences, sequence alignments, and trees.
To create a folder, hover over Shared workspace, click the menu button (3 vertical dots) and click New folder in the popup menu.
Once you’ve created a folder, you can create more Folders within this folder by hovering your mouse over the folder and clicking the menu button.
Files can be moved from one folder to another using the "Move" icon at the top of the document table.
Folders can also be moved by clicking and dragging them to the desired location.
By default, any new folder is not shared until you set up the sharing options. To share folders, select Manage Sharing in the popup menu for folder, which can be accessed by clicking on the menu button (vertical ellipsis).
You can set the access level for all members of your organization as well as add new members by typing your colleagues’ name or email address into the field and select the user you wish to add.
Note that you can only manage sharing of your top level folders. You can find out more about sharing folders here.
Importing and uploading files
Once you have created a folder, files can be uploaded using the Upload button or via drag-and-drop.
For more detail about how file upload works and how to troubleshoot any issues, see here.
If you have Geneious Prime software, you can also try out our beta integration with Prime. The integration enables easy upload of sequences to Biologics from Prime, and allows you to view Biologics sequence documents in Prime. There is more information on how to set the integration up here.
Analyzing NGS data with the Antibody Annotator
To view flowcharts guiding you through the Biologics platform, see this article.
Set and merge paired reads
To pair reads, select a fastq file or multiple fastq files, click Pre-processing and click Set & merge paired read in the dropdown.
To pair corresponding reads, select the appropriate settings for the data and click Run. In this example, the data are paired and merged.
Once the reads are merged, a new document containing the merged reads will be generated (as well as one contained the unmarked ones). To run an NGS analysis with the Antibody annotator, select the merged data, click Annotation and select Antibody Annotator in the dropdown.
Once the appropriate settings have been selected, click Run to start the analysis. You can find out more about the options available here or by clicking the Help button on the bottom right corner of the Antibody annotator popup.
The Antibody annotator will output a result document with the words Annotated & Clustered appended to the end of your input file name.
There is a step-by-step NGS analysis example here.
Running a Sanger Analysis with the Antibody Annotator
Sanger analysis in Geneious Biologics is much the same process as the NGS workflow described above. The main differences are the preprocessing steps used to clean your data prior to running Antibody Annotator, and how you choose to continue your analysis after annotation.
To view flowcharts guiding you through the Biologics platform, see this article.
Preprocessing steps currently used on Sanger sequences include: Batch Assembly, Associate Heavy/Light Chains, Find Heterozygotes, and Batch Rename. These steps can be used alone or in combination.
Note that Batch Assembly and Associate Heavy/Light Chains may require that sequences have consistent naming schemes so that they can be matched correctly. This can be achieved with the Batch rename operation, which renames sequences by replacing or removing existing sections of the name.
If you wish to see parts of your sequence names (such as Well ID) in the annotation Result "All Sequences" table, this can be achieved by setting up a File Naming Scheme. File naming schemes are particularly useful for creating columns to use when adding extra experimental data to your sequences. For more information about adding assay data to your results, see here. You can also add labels and free-form text notes to your sequences after annotation.
Once the analysis is finished, you can visualise the results by selecting the Antibody annotator output file. The Pipeline Report and Graphs tab give an overview of the results which also consist of details on the Heavy and Light CDR3 diversity alongside VJ association in the form of heatmaps. You can export the graphs as pdf files or as .csv files by clicking Export. To learn more see: Using graphs for quality assurance and Using graphs to interpret clusters and clonotypes.
To have a quick overview of the cluster lengths, click the Graphs tab and select Cluster lengths in the dropdown. Then select Heavy CDR3 in the Region dropdown.
Notice that all exports from the graphs are automatically downloaded, while other export operations (such as sequences) need the user to download the exported document from the jobs table (see screenshot below).
To view individual reads, select the NGS analysis output file and select the reads that you would like to have a closer look at. This will open the selected reads in the Sequence Viewer.
You can also view the clusters generated by selecting one from the Cluster Table dropdown menu. In the below example, the Heavy CDR3 cluster table is selected, which will group all sequences together that have the same Heavy CDR3 sequence. To learn more about what clusters are, see this article. Note that multi-region and inexact clusters can also be specified in the clustering options of Antibody Annotator: Clustering Options.
The Annotator Result tables can be filtered by specifying a valid SQL condition using column headers as the fields to filter on.
To search for sequences that meet the condition of having both heavy and light chains with a Heavy CDR3 motif of ‘AKNQGYVFGNWFFDH’, you can either right click an appropriate cell with the selected conditions to filter on or input a syntax as such: ['Heavy CDR3'] = 'ARWEYYAMDY' AND ['Heavy V Gene'] LIKE 'IGHV1%'
Once you have specify your syntax, hit Enter or click Filter. The Sequences Table will refresh and only sequences that fit the specified conditions will be shown in the results table. You can learn more about NGS data filtering and SQL syntax used in Geneious Biologics here.
After filtering, you may choose to extract the subset of sequences that meet your filtering conditions to a new Biologics Annotator Result document. You can do this by choosing the option for Export/Extract in the Sequences Table.
Barcodes, UMIs and Single Cell Analysis
Geneious Biologics supports preprocessing or demultiplexing of sequences with UMIs and/or Barcodes with our Collapse UMIs and Separate Barcodes tool. We also support identification of dominant chains with our Single Clone Analysis tool.
To view flowcharts guiding you through the Biologics platform, see this article. The Single Cell or Single Clone Analysis workflows may also be useful for anyone who is unsure of how to process their data with Biologics. This could be barcoded data where each barcode corresponds to a dominant heavy and light chain pair, or if you have fasta/fastq files where each file is expected to have a dominant chain or pair of chains. This covers a range of different types of experimental processes, including both Single Cell and Single Clone workflows.
Note: This functionality is available as an add-on. If your organisation does not have Barcode Separation, UMI Collapse, or Single Clone Analysis pipelines, please contact us to try them out.
Need more help?