If you are using our Starter plan, please refer to our Getting Started Guide for Starter Plan.
This written guide aims at getting you up and running quickly with Geneious Biologics. Note that this guide is geared towards antibody and antibody-like analysis; if you have generic protein or peptide sequences please see our Peptide Tutorial 1 or our main article on the Peptide Annotator.
You can find our series of introductory tutorial videos here, with the first one below:
The written guide for getting up-and-running with Biologics follows:
- Adding users
- Workspace and Folders
- Folder sharing
- Importing and uploading files
- Analyzing NGS sequences with NGS Antibody Annotator
- Analyzing Sanger Sequences with Antibody Annotator
- 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. We also have a set of Tutorials that can be followed.
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).
Signing in
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. If you are having issues logging in see Accessing Geneious Biologics.
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.
Folder sharing
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 NGS Antibody Annotator
Often the workflow consists of:
- Pairing and merging the R1 and R2 read files
- Running NGS Antibody Annotator
View our Workflows and Flowcharts for Antibody Analysis for more pathways.
Set and merge paired reads
To pair reads, select a fastq file or multiple fastq files, click Pre-processing > Set & Merge Paired Reads 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.
You can find out more about the Set & Merge Paired Reads operation in the following Knowledge Base articles: Set paired reads and Merge paired reads.
NGS Antibody Annotator
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 NGS 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 on our main page NGS Antibody Annotator.
The NGS Antibody Annotator will output a result document in the same folder (unless otherwise specified) with the words Annotated & Clustered appended to the end of your input file name. To learn more, jump to the Visualizing results section.
There is a step-by-step NGS analysis example: NGS Tutorial 1. Sequence Analysis.
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.
Preprocessing steps
-
Group Sequences
- Used to group individual sequences into a sequence list
-
Batch Assembly
- Assemble fwd and rev reads + pair chains. See using Name Schemes below
- Associate Heavy/Light Chains
- Find Heterozygotes
The above steps can be used alone or in combination. We also have Workflows and Flowcharts for Antibody Analysis.
Batch Assembly and Associate Heavy/Light Chains may require that sequences have consistent naming formats so that they can be matched correctly. The information in the sequence names can be pulled out using a Name Scheme.
- You can also use the Batch rename operation to rename sequences by replacing or removing existing sections of the name
Name Schemes
If you wish to pair heavy light chains and/or see parts of your sequence names (such as Well ID) in the annotation result, this can be achieved by setting up a Name Scheme.
Name schemes are particularly useful for pairing your chains and creating columns to use when adding extra experimental data to your sequences.
For more information about adding assay data to your results, see
- Adding Assay Data to your Analysis Results
- You can also add labels and free-form text notes to your sequences after annotation
We have several tutorials for Sanger Analysis available, including one focusing on chromatogram data and the other on paired Heavy and Light chain data.
Visualizing results
Once an analysis has finished running, you can visualise the results by opening the Biologics Annotator Result output file. Graphs pertaining to the dataset and clusters will be automatically viewable in a window below the dataset and cluster tables:
You can also switch to the Pipeline Report and Graphs tabs to give an overview of the results and view the graphs in a full window.
To learn more see:
Graphs can be exported as pdf files or as .csv files by clicking Export:
All exports are automatically downloaded by default. Exported files can also be downloaded from the jobs table, shown below (2).
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:
To view individual reads, return to the Sequences Table and select the reads that you would like to have a closer look at. This will open the selected reads in the Sequence Viewer panel:
You can also view the clusters generated by selecting one from the Cluster Table dropdown menu (highlighted above). In the example above, 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 Understanding "Clusters". You can also Add Clusters to your Results.
Note that multi-region and inexact clusters can also be specified in the clustering options of Antibody Annotator: Clustering Options.
Data Filtering
The Annotator Result tables can be filtered by specifying a valid SQL condition using column headers as the fields to filter on.
In the example above, right clicking on the value in the Table and selecting the suggested filter:
['ASSAY_DATA_Biophysical_Assays:Fab Tm by DSF (°C)'] = 62.5
Will add the above to the filter bar. You can then edit this value in the filter bar by:
- Changing the operator of equals (=) to something else
- Changing the values
- Layer filters by right clicking on other cells and adding. This adds filters with the AND qualifier.
For our full article, see Filtering your Sequences.
Once you have specified 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.
Further Analysis
Many operations are available to enable you to do more with your datasets, and are accessed via our Export/Extract, Add Metadata or Post-processing drop-downs.
For example, 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 Extract and Recluster via the Export/Extract dropdown:
Other functions under the dropdowns include:
-
Add Assay Data to your Analysis Results via the Add Metadata dropdown
- Perform an Alignment via the Post-processing dropdown
- Add Clusters to your Results via the Post-processing dropdown
- Repair low-quality sequences via the Post-processing dropdown
- Search against an existing collection of sequences or add the selected sequences to a collection via the Post-processing dropdown
It is also possible to compare results across multiple experiments like panning rounds by selecting multiple Biologics Annotator Result documents in the main folder view:
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 Cell Analysis tool.
To view flowcharts guiding you through the Biologics platform, see this article. The Single Cell 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.
There is also a tutorial demonstrating the use of UMIs and Barcodes: NGS Tutorial 3. Using Barcodes and UMIs. This is a 10X Antibody Analysis example, but the same tools can be configured for other non-10X UMI and Barcode applications.
Need more help?
For further questions, please check many other articles in our knowledge base or submit a help request by navigating to our main support page, and then clicking Contact Support.